diff --git a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.paste.test.tsx b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.paste.test.tsx
index 24c38e7c..948a8c6d 100644
--- a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.paste.test.tsx
+++ b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.paste.test.tsx
@@ -47,10 +47,10 @@ beforeEach(() => {
   vi.clearAllMocks();
 });
 
-describe('ReactionEntityForm — Paste Chunk filtering', () => {
-  it('submits the filtered chunk, dropping fields the sidebar excludes (e.g. recordModified)', async () => {
-    // A clipboard chunk that includes recordModified — which the Provenance sidebar filters out
-    // (it is edited in its own sidebar) — plus an ordinary field that must survive the paste.
+describe('ReactionEntityForm — Paste Chunk fill-empty (#589)', () => {
+  it("fills the destination's blanks from the chunk but never pastes separately-managed metadata", async () => {
+    // A clipboard chunk that includes recordModified — auto-managed metadata that must never be
+    // pasted (#704) — plus a doi the (blank) destination should be filled with.
     pasteReactionPartMock.mockResolvedValue([
       { doi: '10.0000/paste-test', recordModified: { time: { value: 'leaked' } } },
       'clipboard-text',
@@ -72,8 +72,10 @@ describe('ReactionEntityForm — Paste Chunk filtering', () => {
     await waitFor(() => expect(addUpdateReactionFieldMock).toHaveBeenCalled());
 
     const { newValue } = addUpdateReactionFieldMock.mock.calls[0][0] as { newValue: Record<string, unknown> };
-    // The bug submitted the raw chunk, leaking recordModified into the merge; the fix submits filtered values.
-    expect(newValue).not.toHaveProperty('recordModified');
+    // The blank doi is filled from the chunk...
     expect(newValue).toHaveProperty('doi', '10.0000/paste-test');
+    // ...but the chunk's recordModified is not applied (it's separately-managed metadata, and the
+    // pasted "leaked" value never reaches the merge).
+    expect(JSON.stringify(newValue)).not.toContain('leaked');
   });
 });
diff --git a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.tsx b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.tsx
index 932bced5..a738c6fb 100644
--- a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.tsx
+++ b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/ReactionEntityForm.tsx
@@ -25,7 +25,7 @@ import { useCallback, useContext, useEffect, useMemo, useState } from 'react';
 import type { ReactionEntityContext } from 'features/reactions/ReactionEntities/reactionEntities.types.ts';
 import type { ReactionSidebarInfo } from 'features/reactions/ReactionEntities/sidebarInfo/sidebarInfo.types.ts';
 import { reactionContext } from '../../reactions.context.ts';
-import { copyReactionPart } from './reactionEntityForm.utils.ts';
+import { copyReactionPart, fillEmptyDeepMerge } from './reactionEntityForm.utils.ts';
 import { ReactionEntityPaste } from './ReactionEntityPaste.tsx';
 import { useDisclosure } from '@mantine/hooks';
 import { showNotification } from 'common/utils/showNotification.tsx';
@@ -110,12 +110,14 @@ export function ReactionEntityForm({
   const onPasteChunk = useCallback(
     (reactionPart: object) => {
       try {
-        // Submit the filtered values, not the raw clipboard chunk: fields the sidebar excludes
-        // (e.g. setup.automationCode, provenance.recordModified, product.measurements) are edited
-        // in their own sidebars and must not be merged in here, or they get duplicated/retained.
-        const formValues = filterValues(reactionPart);
-        form.setValues(formValues);
-        onSubmit(formValues);
+        // Fill the destination's blank fields from the pasted chunk without clobbering values the
+        // user already set, and without pulling in separately-managed metadata (automationCode,
+        // recordModified, measurements — see PASTE_PRESERVED_FIELDS). The form only renders its
+        // managed subset (filterValues), but we persist the full merged entity so pasted
+        // structure/identifiers the form doesn't itself show are saved too. (#589)
+        const merged = fillEmptyDeepMerge(reactionPartWithNestedEntities, reactionPart);
+        form.setValues(filterValues(merged));
+        onSubmit(merged);
         setFormKey(crypto.randomUUID());
       } catch (_e: unknown) {
         showNotification({
@@ -124,7 +126,7 @@ export function ReactionEntityForm({
         });
       }
     },
-    [filterValues, form, onSubmit],
+    [filterValues, form, onSubmit, reactionPartWithNestedEntities],
   );
 
   return (
diff --git a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.test.ts b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.test.ts
index b7e1c186..9dc40eb1 100644
--- a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.test.ts
+++ b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.test.ts
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 import { describe, it, expect, vi, afterEach } from 'vitest';
-import { copyReactionPart, pasteReactionPart } from './reactionEntityForm.utils.ts';
+import { copyReactionPart, fillEmptyDeepMerge, pasteReactionPart } from './reactionEntityForm.utils.ts';
 import { ReactionNodeEntity } from 'store/entities/reactions/reactions.types.ts';
 import { ordNotesToReaction } from 'store/entities/reactions/reactionNotes/reactionNotes.converters.ts';
 
@@ -76,3 +76,43 @@ describe('pasteReactionPart', () => {
     expect(await pasteReactionPart(ReactionNodeEntity.Notes)).toEqual([null, '']);
   });
 });
+
+describe('fillEmptyDeepMerge (Paste Chunk fill-empty semantics, #589)', () => {
+  it("fills the destination's blank fields from the source", () => {
+    const dest = { reactionRole: 'REACTANT', molBlockIdentifiers: [], amount: {} };
+    const source = { reactionRole: 'PRODUCT', molBlockIdentifiers: [{ value: 'MOL' }], amount: { value: '5' } };
+    // Blank arrays/objects in the destination are filled; a value the destination already set is kept.
+    expect(fillEmptyDeepMerge(dest, source)).toEqual({
+      reactionRole: 'REACTANT',
+      molBlockIdentifiers: [{ value: 'MOL' }],
+      amount: { value: '5' },
+    });
+  });
+
+  it('keeps a structure the destination already has rather than replacing it', () => {
+    const dest = { molBlockIdentifiers: [{ value: 'EXISTING' }] };
+    const source = { molBlockIdentifiers: [{ value: 'PASTED' }] };
+    expect(fillEmptyDeepMerge(dest, source)).toEqual({ molBlockIdentifiers: [{ value: 'EXISTING' }] });
+  });
+
+  it('treats 0 and false as set (does not overwrite them)', () => {
+    expect(fillEmptyDeepMerge({ isLimiting: false, n: 0 }, { isLimiting: true, n: 9 })).toEqual({
+      isLimiting: false,
+      n: 0,
+    });
+  });
+
+  it('fills nested blanks without clobbering nested set values', () => {
+    const dest = { source: { vendor: 'Acme', catalogId: '' } };
+    const source = { source: { vendor: 'Other', catalogId: 'C-1', lot: 'L-1' } };
+    expect(fillEmptyDeepMerge(dest, source)).toEqual({ source: { vendor: 'Acme', catalogId: 'C-1', lot: 'L-1' } });
+  });
+
+  it('never pastes separately-managed metadata even into a blank destination (#704)', () => {
+    const dest = { doi: '' };
+    const source = { doi: '10.1/x', recordModified: { time: 'leaked' }, automationCode: { v: 'x' }, measurements: [1] };
+    const result = fillEmptyDeepMerge(dest, source);
+    expect(result).toEqual({ doi: '10.1/x' });
+    expect(JSON.stringify(result)).not.toContain('leaked');
+  });
+});
diff --git a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.ts b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.ts
index 0ce5d8db..39936396 100644
--- a/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.ts
+++ b/ui/src/features/reactions/ReactionEntities/ReactionEntityForm/reactionEntityForm.utils.ts
@@ -27,6 +27,48 @@ interface ClipboardMessage {
   value: object;
 }
 
+/**
+ * Fields that are auto-generated or edited in their own dedicated sidebars and must never be
+ * carried over by Paste Chunk, even into an empty destination — pasting them sets wrong metadata
+ * or duplicates separately-managed data (see #704). Everything else is paste-eligible.
+ */
+const PASTE_PRESERVED_FIELDS = new Set(['recordModified', 'automationCode', 'measurements']);
+
+/** A value counts as "not set" (a blank the paste may fill) if it's nullish, an empty string, or an empty array/object. */
+function isUnset(value: unknown): boolean {
+  if (value === undefined || value === null) return true;
+  if (typeof value === 'string') return value.length === 0;
+  if (Array.isArray(value)) return value.length === 0;
+  if (typeof value === 'object') return Object.keys(value as object).length === 0;
+  // Meaningful primitives (0, false, non-empty strings) are "set".
+  return false;
+}
+
+/**
+ * Deep "fill-empty" merge used by Paste Chunk (#589): keep every value the destination has
+ * already set, and only fill the destination's blanks from the pasted source. Non-empty arrays
+ * are kept wholesale (we don't splice source items into a list the user already populated), and
+ * {@link PASTE_PRESERVED_FIELDS} are never taken from the source. This lets a pasted component
+ * bring over its structure/identifiers into an empty target without clobbering anything the user
+ * already entered.
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export function fillEmptyDeepMerge(destination: any, source: any): any {
+  if (isUnset(source)) return destination;
+  if (isUnset(destination)) return source;
+  // Both sides are set. Recurse into plain objects; for primitives and (non-empty) arrays the
+  // destination already has a value, so it wins.
+  if (Array.isArray(destination) || typeof destination !== 'object' || typeof source !== 'object') {
+    return destination;
+  }
+  const result: Record<string, unknown> = { ...destination };
+  for (const key of Object.keys(source)) {
+    if (PASTE_PRESERVED_FIELDS.has(key)) continue;
+    result[key] = fillEmptyDeepMerge(destination[key], source[key]);
+  }
+  return result;
+}
+
 // TODO parse\stringify via ord-schema
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function replacer(_: unknown, value: any): any {