diff --git a/src-tauri/src/pyramid/stale_helpers_upper.rs b/src-tauri/src/pyramid/stale_helpers_upper.rs
index 10b438c3..488878ce 100644
--- a/src-tauri/src/pyramid/stale_helpers_upper.rs
+++ b/src-tauri/src/pyramid/stale_helpers_upper.rs
@@ -3704,12 +3704,7 @@ async fn apply_supersession_manifest(
                     }
                 };
                 let conn = super::db::open_pyramid_connection(Path::new(&db))?;
-                conn.execute(
-                    "UPDATE pyramid_file_hashes
-                     SET hash = ?1, last_ingested_at = datetime('now')
-                     WHERE slug = ?2 AND file_path = ?3",
-                    rusqlite::params![hash, slug_owned, path_owned],
-                )?;
+                super::db::set_file_content_hash(&conn, &slug_owned, &path_owned, &hash)?;
                 Ok(())
             })
             .await
@@ -5279,6 +5274,8 @@ mod tests {
         ChangeManifest, ChildSwap, ContentUpdates, DecisionOp, ManifestValidationError, TermOp,
         TopicOp,
     };
+    use crate::pyramid::understanding_rebuild::rebuild_pyramid_node_metadata_from_store;
+    use crate::pyramid::understanding_store::understanding_root_from_conn;
     use rusqlite::{params, Connection};
     use std::sync::Arc;
     use tempfile::NamedTempFile;
@@ -6637,6 +6634,25 @@ mod tests {
         );
 
         let db_path_str = db_file.path().to_str().unwrap().to_string();
+        {
+            let conn_seed_ids = open_pyramid_db(db_file.path()).expect("reopen db for ids seed");
+            conn_seed_ids
+                .execute(
+                    "UPDATE pyramid_file_hashes
+                     SET node_ids = ?3
+                     WHERE slug = ?1 AND file_path = ?2",
+                    params![
+                        slug,
+                        file_path_str,
+                        serde_json::to_string(&vec![
+                            "L0-targeted".to_string(),
+                            node_id.to_string()
+                        ])
+                        .unwrap(),
+                    ],
+                )
+                .expect("seed multi-node file hash references");
+        }
 
         // Load the node context against the post-edit file. This verifies
         // load_supersession_node_context pulls the source file for L0
@@ -6741,6 +6757,55 @@ mod tests {
             stored_hash, post_edit_hash,
             "pyramid_file_hashes.hash should be rewritten to the post-edit hash so the watcher stops re-firing"
         );
+        let stored_node_ids: String = conn_verify
+            .query_row(
+                "SELECT node_ids FROM pyramid_file_hashes WHERE slug = ?1 AND file_path = ?2",
+                params![slug, file_path_str],
+                |row| row.get(0),
+            )
+            .expect("load post-apply node_ids");
+        let parsed_node_ids: Vec<String> =
+            serde_json::from_str(&stored_node_ids).expect("node_ids json");
+        assert_eq!(
+            parsed_node_ids,
+            vec!["L0-targeted".to_string(), node_id.to_string()],
+            "change-manifest hash rewrite must preserve existing file_hash node_ids"
+        );
+
+        let root = understanding_root_from_conn(&conn_verify).expect("test DB has store root");
+        let mirrored_manifest = crate::pyramid::understanding_store::read_all_node_metadata_records(
+            &root,
+        )
+        .expect("read node-metadata log")
+        .into_iter()
+        .any(|rec| {
+            rec.kind == "change_manifest"
+                && rec.slug == slug
+                && rec.key == format!("{node_id}|2")
+                && rec.op == "upsert"
+        });
+        assert!(
+            mirrored_manifest,
+            "apply path must mirror the change-manifest row before rebuild"
+        );
+        crate::pyramid::db::backfill_node_metadata_to_store(&conn_verify)
+            .expect("backfill fixture metadata so rebuild gate can run");
+        conn_verify
+            .execute("DELETE FROM pyramid_change_manifests", [])
+            .expect("clear change-manifest projection");
+        let rebuilt =
+            rebuild_pyramid_node_metadata_from_store(&root, &conn_verify).expect("rebuild metadata");
+        assert!(
+            rebuilt > 0,
+            "node-metadata rebuild should restore mirrored change-manifest rows"
+        );
+        let manifests = get_change_manifests_for_node(&conn_verify, slug, node_id)
+            .expect("load rebuilt change manifests");
+        assert_eq!(manifests.len(), 1, "change manifest should rebuild from store");
+        assert_eq!(
+            manifests[0].build_version, 2,
+            "rebuilt manifest should preserve post-apply build_version"
+        );
     }
 
     /// Fix pass test 2: manifest-generation failure must NOT fall back to