diff --git a/server/src/main/java/org/eclipse/openvsx/ExtensionService.java b/server/src/main/java/org/eclipse/openvsx/ExtensionService.java
index a39ba2596..2c57003c8 100644
--- a/server/src/main/java/org/eclipse/openvsx/ExtensionService.java
+++ b/server/src/main/java/org/eclipse/openvsx/ExtensionService.java
@@ -207,6 +207,9 @@ public void reactivateExtensions(UserData user) {
         var affectedExtensions = new LinkedHashSet<Extension>();
         var versions = repositories.findVersionsByUser(user, false);
         for (var version : versions) {
+            if (version.getState() == ExtensionVersion.State.DELETED) {
+                continue;
+            }
             version.setActive(true);
             affectedExtensions.add(version.getExtension());
         }
@@ -225,10 +228,20 @@ public ResultJson deleteExtension(
         var results = new ArrayList<ResultJson>();
         if(repositories.isDeleteAllVersions(namespaceName, extensionName, targetVersions, user)) {
             var extension = repositories.findExtension(extensionName, namespaceName);
+            if (extension == null || repositories.countVersions(namespaceName, extensionName) == 0) {
+                var message = "Extension not found: " + NamingUtil.toExtensionId(namespaceName, extensionName);
+                throw new ErrorResultException(message, HttpStatus.NOT_FOUND);
+            }
             results.add(deleteExtension(user, extension));
         } else {
             for (var targetVersion : targetVersions) {
-                var extVersion = repositories.findVersion(user, targetVersion.version(), targetVersion.targetPlatform(), extensionName, namespaceName);
+                var extVersion = repositories.findVersion(
+                        user,
+                        targetVersion.version(),
+                        targetVersion.targetPlatform(),
+                        extensionName,
+                        namespaceName
+                );
                 if (extVersion == null) {
                     var message = "Extension not found: " + NamingUtil.toLogFormat(namespaceName, extensionName, targetVersion.targetPlatform(), targetVersion.version());
                     throw new ErrorResultException(message, HttpStatus.NOT_FOUND);
@@ -275,8 +288,7 @@ protected ResultJson deleteExtension(UserData user, Extension extension) throws
             cache.evictExtensionJsons(deprecatedExtension);
         }
 
-        entityManager.remove(extension);
-        search.removeSearchEntry(extension);
+        updateExtension(extension);
 
         var result = ResultJson.success("Deleted " + NamingUtil.toExtensionId(extension));
         logs.logAction(user, result);
@@ -286,7 +298,6 @@ protected ResultJson deleteExtension(UserData user, Extension extension) throws
     protected ResultJson deleteExtension(UserData user, ExtensionVersion extVersion) {
         var extension = extVersion.getExtension();
         removeExtensionVersion(extVersion);
-        extension.getVersions().remove(extVersion);
         updateExtension(extension);
 
         var result = ResultJson.success("Deleted " + NamingUtil.toLogFormat(extVersion));
@@ -301,6 +312,6 @@ private void removeExtensionVersion(ExtensionVersion extVersion) {
         
         repositories.findFiles(extVersion).map(RemoveFileJobRequest::new).forEach(scheduler::enqueue);
         repositories.deleteFiles(extVersion);
-        entityManager.remove(extVersion);
+        extVersion.setState(ExtensionVersion.State.DELETED);
     }
 }
\ No newline at end of file
diff --git a/server/src/main/java/org/eclipse/openvsx/admin/AdminService.java b/server/src/main/java/org/eclipse/openvsx/admin/AdminService.java
index 6ca170c68..ef1ae55ae 100644
--- a/server/src/main/java/org/eclipse/openvsx/admin/AdminService.java
+++ b/server/src/main/java/org/eclipse/openvsx/admin/AdminService.java
@@ -164,8 +164,7 @@ public void deleteExtensionAndDependencies(Extension extension, UserData admin,
             cache.evictExtensionJsons(deprecatedExtension);
         }
 
-        entityManager.remove(extension);
-        search.removeSearchEntry(extension);
+        extensions.updateExtension(extension);
         logs.logAction(admin, ResultJson.success("Deleted " + NamingUtil.toExtensionId(extension)));
     }
 
@@ -177,7 +176,6 @@ protected void deleteExtensionAndDependencies(ExtensionVersion extVersion, UserD
         }
 
         removeExtensionVersion(extVersion);
-        extension.getVersions().remove(extVersion);
         extensions.updateExtension(extension);
         logs.logAction(admin, ResultJson.success("Deleted " + NamingUtil.toLogFormat(extVersion)));
     }
@@ -208,7 +206,7 @@ public ResultJson deleteExtension(
     public ResultJson deleteExtension(String namespaceName, String extensionName, UserData admin)
             throws ErrorResultException {
         var extension = repositories.findExtension(extensionName, namespaceName);
-        if (extension == null) {
+        if (extension == null || repositories.countVersions(namespaceName, extensionName) == 0) {
             var extensionId = NamingUtil.toExtensionId(namespaceName, extensionName);
             throw new ErrorResultException("Extension not found: " + extensionId, HttpStatus.NOT_FOUND);
         }
@@ -259,8 +257,7 @@ protected ResultJson deleteExtension(Extension extension, UserData admin) throws
             cache.evictExtensionJsons(deprecatedExtension);
         }
 
-        entityManager.remove(extension);
-        search.removeSearchEntry(extension);
+        extensions.updateExtension(extension);
 
         var result = ResultJson.success("Deleted " + NamingUtil.toExtensionId(extension));
         logs.logAction(admin, result);
@@ -270,7 +267,6 @@ protected ResultJson deleteExtension(Extension extension, UserData admin) throws
     protected ResultJson deleteExtension(ExtensionVersion extVersion, UserData admin) {
         var extension = extVersion.getExtension();
         removeExtensionVersion(extVersion);
-        extension.getVersions().remove(extVersion);
         extensions.updateExtension(extension);
 
         var result = ResultJson.success("Deleted " + NamingUtil.toLogFormat(extVersion));
@@ -323,7 +319,7 @@ private void removeExtensionVersion(ExtensionVersion extVersion) {
         
         repositories.findFiles(extVersion).map(RemoveFileJobRequest::new).forEach(scheduler::enqueue);
         repositories.deleteFiles(extVersion);
-        entityManager.remove(extVersion);
+        extVersion.setState(ExtensionVersion.State.DELETED);
     }
 
     private String userNotFoundMessage(String user) {
diff --git a/server/src/main/java/org/eclipse/openvsx/entities/ExtensionVersion.java b/server/src/main/java/org/eclipse/openvsx/entities/ExtensionVersion.java
index 6814181d4..a5c23768e 100644
--- a/server/src/main/java/org/eclipse/openvsx/entities/ExtensionVersion.java
+++ b/server/src/main/java/org/eclipse/openvsx/entities/ExtensionVersion.java
@@ -79,6 +79,13 @@ public enum State {
     @ManyToOne
     private PersonalAccessToken publishedWith;
 
+    /**
+     * Legacy persisted mirror of {@link #state} kept for compatibility with active-based queries.
+     *
+     * @deprecated Use {@link #getState()} / {@link #setState(State)}. This field is planned for
+     *             removal once repositories and SQL queries fully migrate to state-based filtering.
+     */
+    @Deprecated(forRemoval = true)
     private boolean active;
 
     @Enumerated(EnumType.STRING)
@@ -322,10 +329,18 @@ public void setPublishedWith(PersonalAccessToken publishedWith) {
         this.publishedWith = publishedWith;
     }
 
+    /**
+     * @deprecated Use {@code getState() == State.ACTIVE}.
+     */
+    @Deprecated(forRemoval = true)
     public boolean isActive() {
         return state == State.ACTIVE;
     }
 
+    /**
+     * @deprecated Use {@link #setState(State)} with {@link State#ACTIVE} or {@link State#INACTIVE}.
+     */
+    @Deprecated(forRemoval = true)
     public void setActive(boolean active) {
         setState(active ? State.ACTIVE : State.INACTIVE);
     }
diff --git a/server/src/main/java/org/eclipse/openvsx/publish/PublishExtensionVersionHandler.java b/server/src/main/java/org/eclipse/openvsx/publish/PublishExtensionVersionHandler.java
index 14dd66e69..a9b559e84 100644
--- a/server/src/main/java/org/eclipse/openvsx/publish/PublishExtensionVersionHandler.java
+++ b/server/src/main/java/org/eclipse/openvsx/publish/PublishExtensionVersionHandler.java
@@ -169,7 +169,7 @@ private ExtensionVersion createExtensionVersion(ExtensionProcessor processor, Us
 
             entityManager.persist(extension);
         } else {
-            var existingVersion = repositories.findVersion(extVersion.getVersion(), extVersion.getTargetPlatform(), extension);
+            var existingVersion = repositories.findVersionIncludingDeleted(extVersion.getVersion(), extVersion.getTargetPlatform(), extension);
             if (existingVersion != null) {
                 var extVersionId = NamingUtil.toLogFormat(namespaceName, extensionName, extVersion.getTargetPlatform(), extVersion.getVersion());
                 var message = "Extension " + extVersionId + " is already published";
diff --git a/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionJooqRepository.java b/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionJooqRepository.java
index b90d91136..ffe3e1708 100644
--- a/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionJooqRepository.java
+++ b/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionJooqRepository.java
@@ -477,19 +477,22 @@ private ExtensionVersion toExtensionVersionFull(
             newNamespace.setPublicId(row.get(NAMESPACE.PUBLIC_ID));
         }
 
-        var user = new UserData();
-        user.setId(row.get(USER_DATA.ID));
-        user.setRole(row.get(USER_DATA.ROLE));
-        user.setLoginName(row.get(USER_DATA.LOGIN_NAME));
-        user.setFullName(row.get(USER_DATA.FULL_NAME));
-        user.setAvatarUrl(row.get(USER_DATA.AVATAR_URL));
-        user.setProviderUrl(row.get(USER_DATA.PROVIDER_URL));
-        user.setProvider(row.get(USER_DATA.PROVIDER));
-
-        var token = new PersonalAccessToken();
-        token.setUser(user);
-
-        extVersion.setPublishedWith(token);
+        var userId = row.get(USER_DATA.ID);
+        if (userId != null) {
+            var user = new UserData();
+            user.setId(userId);
+            user.setRole(row.get(USER_DATA.ROLE));
+            user.setLoginName(row.get(USER_DATA.LOGIN_NAME));
+            user.setFullName(row.get(USER_DATA.FULL_NAME));
+            user.setAvatarUrl(row.get(USER_DATA.AVATAR_URL));
+            user.setProviderUrl(row.get(USER_DATA.PROVIDER_URL));
+            user.setProvider(row.get(USER_DATA.PROVIDER));
+
+            var token = new PersonalAccessToken();
+            token.setUser(user);
+            extVersion.setPublishedWith(token);
+        }
+
         extVersion.setType(ExtensionVersion.Type.REGULAR);
         return extVersion;
     }
@@ -569,6 +572,7 @@ public List<VersionTargetPlatformsJson> findTargetPlatformsGroupedByVersion(Exte
                 )
                 .from(EXTENSION_VERSION)
                 .where(EXTENSION_VERSION.EXTENSION_ID.eq(extension.getId()))
+                .and(EXTENSION_VERSION.STATE.ne(ExtensionVersion.State.DELETED.name()))
                 .groupBy(
                         EXTENSION_VERSION.SEMVER_MAJOR,
                         EXTENSION_VERSION.SEMVER_MINOR,
@@ -609,6 +613,7 @@ public List<VersionTargetPlatformsJson> findTargetPlatformsGroupedByVersion(Exte
                 .join(PERSONAL_ACCESS_TOKEN).on(PERSONAL_ACCESS_TOKEN.ID.eq(EXTENSION_VERSION.PUBLISHED_WITH_ID))
                 .where(EXTENSION_VERSION.EXTENSION_ID.eq(extension.getId()))
                 .and(PERSONAL_ACCESS_TOKEN.USER_DATA.eq(user.getId()))
+                .and(EXTENSION_VERSION.STATE.ne(ExtensionVersion.State.DELETED.name()))
                 .groupBy(
                         EXTENSION_VERSION.SEMVER_MAJOR,
                         EXTENSION_VERSION.SEMVER_MINOR,
@@ -1481,6 +1486,19 @@ public Integer count(String namespaceName, String extensionName) {
                 .fetchOne("count", Integer.class);
     }
 
+    public Integer countNonDeleted(String namespaceName, String extensionName) {
+        return dsl.select(DSL.count().as("count"))
+                .from(EXTENSION_VERSION)
+                .join(EXTENSION)
+                .on(EXTENSION.ID.eq(EXTENSION_VERSION.EXTENSION_ID))
+                .join(NAMESPACE)
+                .on(NAMESPACE.ID.eq(EXTENSION.NAMESPACE_ID))
+                .where(NAMESPACE.NAME.equalIgnoreCase(namespaceName))
+                .and(EXTENSION.NAME.equalIgnoreCase(extensionName))
+                .and(EXTENSION_VERSION.STATE.ne(ExtensionVersion.State.DELETED.name()))
+                .fetchOne("count", Integer.class);
+    }
+
     public boolean isDeleteAllVersions(String namespaceName, String extensionName, List<TargetPlatformVersionJson> targetVersions, UserData user) {
         if(targetVersions.isEmpty()) {
             return false;
@@ -1492,6 +1510,7 @@ public boolean isDeleteAllVersions(String namespaceName, String extensionName, L
                 .join(NAMESPACE).on(NAMESPACE.ID.eq(EXTENSION.NAMESPACE_ID))
                 .and(NAMESPACE.NAME.equalIgnoreCase(namespaceName))
                 .and(EXTENSION.NAME.equalIgnoreCase(extensionName))
+            .and(EXTENSION_VERSION.STATE.ne(ExtensionVersion.State.DELETED.name()))
                 .fetchOne("all", Integer.class);
 
         var rows = targetVersions.stream().map((tv) -> DSL.row(tv.version(), tv.targetPlatform())).toArray(Row2[]::new);
@@ -1507,6 +1526,7 @@ public boolean isDeleteAllVersions(String namespaceName, String extensionName, L
                 .where(PERSONAL_ACCESS_TOKEN.USER_DATA.eq(user.getId()))
                 .and(NAMESPACE.NAME.equalIgnoreCase(namespaceName))
                 .and(EXTENSION.NAME.equalIgnoreCase(extensionName))
+                .and(EXTENSION_VERSION.STATE.ne(ExtensionVersion.State.DELETED.name()))
                 .fetchOne("actual", Integer.class);
 
         return Objects.equals(actual, all);
@@ -1515,10 +1535,10 @@ public boolean isDeleteAllVersions(String namespaceName, String extensionName, L
     public Page<ExtensionVersion> findChanges(LocalDateTime since, LocalDateTime before, int size, int offset) {
         var conditions = new ArrayList<Condition>();
         if (since != null) {
-            conditions.add(EXTENSION_VERSION.TIMESTAMP.greaterOrEqual(since));
+            conditions.add(EXTENSION_VERSION.LAST_UPDATED.greaterOrEqual(since));
         }
         if (before != null) {
-            conditions.add(EXTENSION_VERSION.TIMESTAMP.lessThan(before));
+            conditions.add(EXTENSION_VERSION.LAST_UPDATED.lessThan(before));
         }
 
         var countField = DSL.count();
@@ -1529,7 +1549,7 @@ public Page<ExtensionVersion> findChanges(LocalDateTime since, LocalDateTime bef
 
         var query = baseExtensionVersionQuery();
         query.addConditions(conditions);
-        query.addOrderBy(EXTENSION_VERSION.TIMESTAMP.desc());
+        query.addOrderBy(EXTENSION_VERSION.LAST_UPDATED.desc());
         query.addLimit(size);
         query.addOffset(offset);
 
diff --git a/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionRepository.java b/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionRepository.java
index df07961f2..dfa9fd850 100644
--- a/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionRepository.java
+++ b/server/src/main/java/org/eclipse/openvsx/repositories/ExtensionVersionRepository.java
@@ -27,10 +27,34 @@ public interface ExtensionVersionRepository extends Repository<ExtensionVersion,
 
     ExtensionVersion findByVersionAndTargetPlatformAndExtension(String version, String targetPlatform, Extension extension);
 
+        ExtensionVersion findByVersionAndTargetPlatformAndExtensionAndStateNot(
+            String version,
+            String targetPlatform,
+            Extension extension,
+            ExtensionVersion.State state
+        );
+
     ExtensionVersion findByVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(String version, String targetPlatform, String extensionName, String namespace);
 
+        ExtensionVersion findByVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndStateNot(
+            String version,
+            String targetPlatform,
+            String extensionName,
+            String namespace,
+            ExtensionVersion.State state
+        );
+
     ExtensionVersion findByPublishedWithUserAndVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(UserData user, String version, String targetPlatform, String extensionName, String namespace);
 
+        ExtensionVersion findByPublishedWithUserAndVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndStateNot(
+            UserData user,
+            String version,
+            String targetPlatform,
+            String extensionName,
+            String namespace,
+            ExtensionVersion.State state
+        );
+
     Streamable<ExtensionVersion> findByVersionAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(String version, String extensionName, String namespace);
 
     Streamable<ExtensionVersion> findByPublishedWithAndActive(PersonalAccessToken publishedWith, boolean active);
@@ -41,11 +65,21 @@ public interface ExtensionVersionRepository extends Repository<ExtensionVersion,
 
     Streamable<ExtensionVersion> findBySignatureKeyPairNotOrSignatureKeyPairIsNull(SignatureKeyPair keyPair);
 
-    @Query("select ev from ExtensionVersion ev where concat(',', ev.bundledExtensions, ',') like concat('%,', ?1, ',%')")
-    Streamable<ExtensionVersion> findByBundledExtensions(String extensionId);
-
-    @Query("select ev from ExtensionVersion ev where concat(',', ev.dependencies, ',') like concat('%,', ?1, ',%')")
-    Streamable<ExtensionVersion> findByDependencies(String extensionId);
+        @Query("""
+            select ev
+            from ExtensionVersion ev
+            where concat(',', ev.bundledExtensions, ',') like concat('%,', ?1, ',%')
+            and ev.state <> ?2
+            """)
+        Streamable<ExtensionVersion> findByBundledExtensionsAndStateNot(String extensionId, ExtensionVersion.State state);
+
+        @Query("""
+            select ev
+            from ExtensionVersion ev
+            where concat(',', ev.dependencies, ',') like concat('%,', ?1, ',%')
+            and ev.state <> ?2
+            """)
+        Streamable<ExtensionVersion> findByDependenciesAndStateNot(String extensionId, ExtensionVersion.State state);
 
     @Query("select min(ev.timestamp) from ExtensionVersion ev")
     LocalDateTime getOldestTimestamp();
@@ -56,5 +90,18 @@ public interface ExtensionVersionRepository extends Repository<ExtensionVersion,
 
     Page<ExtensionVersion> findByExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(String extension, String namespace, Pageable page);
 
+        Page<ExtensionVersion> findByExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndActiveTrue(
+            String extension,
+            String namespace,
+            Pageable page
+        );
+
     Page<ExtensionVersion> findByTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(String targetPlatform, String extension, String namespace, Pageable page);
+
+        Page<ExtensionVersion> findByTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndActiveTrue(
+            String targetPlatform,
+            String extension,
+            String namespace,
+            Pageable page
+        );
 }
\ No newline at end of file
diff --git a/server/src/main/java/org/eclipse/openvsx/repositories/RepositoryService.java b/server/src/main/java/org/eclipse/openvsx/repositories/RepositoryService.java
index b6b1e073d..25e3d7946 100644
--- a/server/src/main/java/org/eclipse/openvsx/repositories/RepositoryService.java
+++ b/server/src/main/java/org/eclipse/openvsx/repositories/RepositoryService.java
@@ -209,14 +209,44 @@ public int getMaxExtensionDownloadCount() {
     }
 
     public ExtensionVersion findVersion(String version, String targetPlatform, Extension extension) {
+        return extensionVersionRepo.findByVersionAndTargetPlatformAndExtensionAndStateNot(
+                version,
+                targetPlatform,
+                extension,
+                ExtensionVersion.State.DELETED
+        );
+    }
+
+    public ExtensionVersion findVersionIncludingDeleted(String version, String targetPlatform, Extension extension) {
         return extensionVersionRepo.findByVersionAndTargetPlatformAndExtension(version, targetPlatform, extension);
     }
 
     public ExtensionVersion findVersion(String version, String targetPlatform, String extensionName, String namespace) {
+        return extensionVersionRepo.findByVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndStateNot(
+                version,
+                targetPlatform,
+                extensionName,
+                namespace,
+                ExtensionVersion.State.DELETED
+        );
+    }
+
+    public ExtensionVersion findVersionIncludingDeleted(String version, String targetPlatform, String extensionName, String namespace) {
         return extensionVersionRepo.findByVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(version, targetPlatform, extensionName, namespace);
     }
 
     public ExtensionVersion findVersion(UserData user, String version, String targetPlatform, String extensionName, String namespace) {
+        return extensionVersionRepo.findByPublishedWithUserAndVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndStateNot(
+                user,
+                version,
+                targetPlatform,
+                extensionName,
+                namespace,
+                ExtensionVersion.State.DELETED
+        );
+    }
+
+    public ExtensionVersion findVersionIncludingDeleted(UserData user, String version, String targetPlatform, String extensionName, String namespace) {
         return extensionVersionRepo.findByPublishedWithUserAndVersionAndTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(user, version, targetPlatform, extensionName, namespace);
     }
 
@@ -229,11 +259,20 @@ public Streamable<ExtensionVersion> findActiveVersions(Extension extension) {
     }
 
     public Page<ExtensionVersion> findActiveVersionsSorted(String namespace, String extension, PageRequest page) {
-        return extensionVersionRepo.findByExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(extension, namespace, page.withSort(VERSIONS_SORT));
+        return extensionVersionRepo.findByExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndActiveTrue(
+                extension,
+                namespace,
+                page.withSort(VERSIONS_SORT)
+        );
     }
 
     public Page<ExtensionVersion> findActiveVersionsSorted(String namespace, String extension, String targetPlatform, PageRequest page) {
-        return extensionVersionRepo.findByTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCase(targetPlatform, extension, namespace, page.withSort(VERSIONS_SORT));
+        return extensionVersionRepo.findByTargetPlatformAndExtensionNameIgnoreCaseAndExtensionNamespaceNameIgnoreCaseAndActiveTrue(
+                targetPlatform,
+                extension,
+                namespace,
+                page.withSort(VERSIONS_SORT)
+        );
     }
 
     public Page<String> findActiveVersionStringsSorted(String namespace, String extension, String targetPlatform, PageRequest page) {
@@ -253,11 +292,17 @@ public List<ExtensionVersion> findActiveVersionReferencesSorted(Collection<Long>
     }
 
     public Streamable<ExtensionVersion> findBundledExtensionsReference(Extension extension) {
-        return extensionVersionRepo.findByBundledExtensions(NamingUtil.toExtensionId(extension));
+        return extensionVersionRepo.findByBundledExtensionsAndStateNot(
+                NamingUtil.toExtensionId(extension),
+                ExtensionVersion.State.DELETED
+        );
     }
 
     public Streamable<ExtensionVersion> findDependenciesReference(Extension extension) {
-        return extensionVersionRepo.findByDependencies(NamingUtil.toExtensionId(extension));
+        return extensionVersionRepo.findByDependenciesAndStateNot(
+                NamingUtil.toExtensionId(extension),
+                ExtensionVersion.State.DELETED
+        );
     }
 
     public Streamable<Extension> findExtensions(UserData user) {
@@ -513,6 +558,10 @@ public Streamable<ExtensionVersion> findTargetPlatformVersions(String version, S
     }
 
     public int countVersions(String namespaceName, String extensionName) {
+        return extensionVersionJooqRepo.countNonDeleted(namespaceName, extensionName);
+    }
+
+    public int countAllVersions(String namespaceName, String extensionName) {
         return extensionVersionJooqRepo.count(namespaceName, extensionName);
     }
 
diff --git a/server/src/main/java/org/eclipse/openvsx/scanning/ExtensionScanCompletionService.java b/server/src/main/java/org/eclipse/openvsx/scanning/ExtensionScanCompletionService.java
index 738754c7d..f28b1dacf 100644
--- a/server/src/main/java/org/eclipse/openvsx/scanning/ExtensionScanCompletionService.java
+++ b/server/src/main/java/org/eclipse/openvsx/scanning/ExtensionScanCompletionService.java
@@ -685,6 +685,12 @@ public boolean adminAllowScan(ExtensionScan scan) {
                     detachedVersion.getId(), scan.getId());
                 return false;
             }
+
+            if (extVersion.getState() == ExtensionVersion.State.DELETED) {
+                logger.warn("Cannot activate deleted extension version for scan #{}: {}",
+                    scan.getId(), NamingUtil.toLogFormat(extVersion));
+                return false;
+            }
             
             // Already active - just mark scan passed
             if (extVersion.isActive()) {
diff --git a/server/src/main/java/org/eclipse/openvsx/search/SimilarityCheckService.java b/server/src/main/java/org/eclipse/openvsx/search/SimilarityCheckService.java
index 2fe021646..5453f5755 100644
--- a/server/src/main/java/org/eclipse/openvsx/search/SimilarityCheckService.java
+++ b/server/src/main/java/org/eclipse/openvsx/search/SimilarityCheckService.java
@@ -82,7 +82,7 @@ public PublishCheck.Result check(PublishCheck.Context context) {
         var extensionName = scan.getExtensionName();
         var displayName = scan.getExtensionDisplayName();
 
-        if (config.isOnlyCheckNewExtensions() && repositories.countVersions(namespaceName, extensionName) > 0) {
+        if (config.isOnlyCheckNewExtensions() && repositories.countAllVersions(namespaceName, extensionName) > 0) {
             return PublishCheck.Result.pass();
         }
 
diff --git a/server/src/test/java/org/eclipse/openvsx/RegistryAPITest.java b/server/src/test/java/org/eclipse/openvsx/RegistryAPITest.java
index 0726f4578..b1d0307fd 100644
--- a/server/src/test/java/org/eclipse/openvsx/RegistryAPITest.java
+++ b/server/src/test/java/org/eclipse/openvsx/RegistryAPITest.java
@@ -1700,6 +1700,17 @@ void testPublishExistingExtension() throws Exception {
                 .andExpect(content().json(errorJson("Extension foo.bar 1.0.0 is already published.")));
     }
 
+    @Test
+    void testPublishDeletedExtensionVersion() throws Exception {
+        mockForPublish("existing-inactive");
+        var bytes = createExtensionPackage("bar", "1.0.0", null);
+        mockMvc.perform(post("/api/-/publish?token={token}", "my_token")
+                .contentType(MediaType.APPLICATION_OCTET_STREAM)
+                .content(bytes))
+                .andExpect(status().isBadRequest())
+                .andExpect(content().json(errorJson("Extension foo.bar 1.0.0 is already published, but currently isn't active and therefore not visible.")));
+    }
+
     @Test
     void testPublishSameVersionDifferentTargetPlatformPreRelease() throws Exception {
         var extVersion = mockExtension(TargetPlatform.NAME_WIN32_X64);
@@ -2502,16 +2513,20 @@ private void mockForPublish(String mode) {
         namespace.setName("foo");
         Mockito.when(repositories.findNamespace("foo"))
                 .thenReturn(namespace);
-        if (mode.equals("existing")) {
+        if (mode.equals("existing") || mode.equals("existing-inactive")) {
             var extension = new Extension();
             extension.setName("bar");
             var extVersion = new ExtensionVersion();
             extVersion.setTargetPlatform(TargetPlatform.NAME_UNIVERSAL);
             extVersion.setVersion("1.0.0");
-            extVersion.setActive(true);
+            if (mode.equals("existing-inactive")) {
+                extVersion.setState(ExtensionVersion.State.DELETED);
+            } else {
+                extVersion.setActive(true);
+            }
             Mockito.when(repositories.findExtension("bar", namespace))
                     .thenReturn(extension);
-            Mockito.when(repositories.findVersion("1.0.0", TargetPlatform.NAME_UNIVERSAL, extension))
+                Mockito.when(repositories.findVersionIncludingDeleted("1.0.0", TargetPlatform.NAME_UNIVERSAL, extension))
                     .thenReturn(extVersion);
         }
         Mockito.when(repositories.countActiveReviews(any(Extension.class)))
@@ -2536,7 +2551,7 @@ private void mockForPublish(String mode) {
             // Mock findMemberships(user) for similarity check
             Mockito.when(repositories.findMemberships(token.getUser()))
                     .thenReturn(Streamable.of(ownerMem));
-        } else if (mode.equals("contributor") || mode.equals("sole-contributor") || mode.equals("existing")) {
+        } else if (mode.equals("contributor") || mode.equals("sole-contributor") || mode.equals("existing") || mode.equals("existing-inactive")) {
             Mockito.when(repositories.canPublishInNamespace(token.getUser(), namespace))
                     .thenReturn(true);
             Mockito.when(repositories.isVerified(namespace, token.getUser()))
diff --git a/server/src/test/java/org/eclipse/openvsx/UserAPITest.java b/server/src/test/java/org/eclipse/openvsx/UserAPITest.java
index 8934cbb4f..bf1a59193 100644
--- a/server/src/test/java/org/eclipse/openvsx/UserAPITest.java
+++ b/server/src/test/java/org/eclipse/openvsx/UserAPITest.java
@@ -730,6 +730,8 @@ private List<ExtensionVersion> mockExtension(UserData user, int numberOfVersions
         extension.getVersions().addAll(versions);
         Mockito.when(repositories.findVersions(extension))
                 .thenReturn(Streamable.of(versions));
+        Mockito.when(repositories.countVersions(namespace.getName(), extension.getName()))
+                .thenReturn(numberOfVersions);
         Mockito.when(repositories.findLatestVersions(user)).thenReturn(List.of(versions.get(versions.size() - 1)));
         Mockito.when(repositories.isDeleteAllVersions(eq("foobar"), eq("baz"), any(List.class), eq(user))).then(new Answer<Boolean>() {
             @Override
diff --git a/server/src/test/java/org/eclipse/openvsx/repositories/RepositoryServiceSmokeTest.java b/server/src/test/java/org/eclipse/openvsx/repositories/RepositoryServiceSmokeTest.java
index 0c79034dd..cf0b1a17a 100644
--- a/server/src/test/java/org/eclipse/openvsx/repositories/RepositoryServiceSmokeTest.java
+++ b/server/src/test/java/org/eclipse/openvsx/repositories/RepositoryServiceSmokeTest.java
@@ -192,11 +192,15 @@ void testExecuteQueries() {
                 () -> repositories.findUsersByLoginNameStartingWith("loginNameStart", 1),
                 () -> repositories.findVersion("version", "targetPlatform", extension),
                 () -> repositories.findVersion("version", "targetPlatform", "extensionName", "namespace"),
+                () -> repositories.findVersionIncludingDeleted("version", "targetPlatform", extension),
                 () -> repositories.findVersions(extension),
+                () -> repositories.findVersionIncludingDeleted("version", "targetPlatform", "extensionName", "namespace"),
                 () -> repositories.findVersionsByAccessToken(personalAccessToken, true),
                 () -> repositories.getMaxExtensionDownloadCount(),
                 () -> repositories.getOldestExtensionTimestamp(),
+                () -> repositories.countAllVersions("namespaceName", "extensionName"),
                 () -> repositories.findExtensions(LONG_LIST),
+                () -> repositories.findVersionIncludingDeleted(userData, "version", "targetPlatform", "extensionName", "namespace"),
                 () -> repositories.findExtensions(userData),
                 () -> repositories.findFilesByType(List.of(extVersion), STRING_LIST),
                 () -> repositories.countVersions("namespaceName", "extensionName"),
diff --git a/server/src/test/java/org/eclipse/openvsx/search/SimilarityCheckServiceTest.java b/server/src/test/java/org/eclipse/openvsx/search/SimilarityCheckServiceTest.java
index 863c2c207..27fc4b70a 100644
--- a/server/src/test/java/org/eclipse/openvsx/search/SimilarityCheckServiceTest.java
+++ b/server/src/test/java/org/eclipse/openvsx/search/SimilarityCheckServiceTest.java
@@ -148,13 +148,13 @@ void shouldDelegateSimilarExtensionsToService() {
     void shouldSkipCheckForExistingExtensionWhenConfiguredForNewOnly() {
         // When configured for new extensions only, skip if extension already has versions (>1 means existing).
         when(config.isOnlyCheckNewExtensions()).thenReturn(true);
-        when(repositories.countVersions("ns", "ext")).thenReturn(2);
+        when(repositories.countAllVersions("ns", "ext")).thenReturn(2);
 
         var context = createContext("ns", "ext", "Display");
         var result = similarityCheckService.check(context);
 
         assertThat(result.passed()).isTrue();
-        verify(repositories).countVersions("ns", "ext");
+        verify(repositories).countAllVersions("ns", "ext");
         verifyNoInteractions(similarityService);
     }
 
@@ -165,7 +165,7 @@ void shouldCheckNewExtensionEvenWhenConfiguredForNewOnly() {
         when(config.isAllowSimilarityToOwnNames()).thenReturn(false);
         when(config.getSimilarityThreshold()).thenReturn(0.15);
         when(config.isOnlyProtectVerifiedNames()).thenReturn(false);
-        when(repositories.countVersions("ns", "ext")).thenReturn(0);
+        when(repositories.countAllVersions("ns", "ext")).thenReturn(0);
         when(similarityService.findSimilarExtensions("ext", "ns", "Display", List.of(), 0.15, false, 10))
                 .thenReturn(List.of());
 
@@ -173,7 +173,7 @@ void shouldCheckNewExtensionEvenWhenConfiguredForNewOnly() {
         var result = similarityCheckService.check(context);
 
         assertThat(result.passed()).isTrue();
-        verify(repositories).countVersions("ns", "ext");
+        verify(repositories).countAllVersions("ns", "ext");
         verify(similarityService).findSimilarExtensions("ext", "ns", "Display", List.of(), 0.15, false, 10);
     }