diff --git a/apps/sim/lib/knowledge/connectors/sync-engine.test.ts b/apps/sim/lib/knowledge/connectors/sync-engine.test.ts
index 23e5d5fa564..dbb58359347 100644
--- a/apps/sim/lib/knowledge/connectors/sync-engine.test.ts
+++ b/apps/sim/lib/knowledge/connectors/sync-engine.test.ts
@@ -515,6 +515,23 @@ describe('classifyExternalDoc', () => {
     ).toEqual({ type: 'update', existingId: 'doc-1' })
   })
 
+  it('uses the same skip replacement rule after deferred hydration', async () => {
+    const { shouldReplaceExistingWithSkippedDocument } = await import(
+      '@/lib/knowledge/connectors/sync-engine'
+    )
+
+    expect(shouldReplaceExistingWithSkippedDocument({ storageKey: null }, {})).toBe(true)
+    expect(shouldReplaceExistingWithSkippedDocument({ storageKey: 'kb/indexed.txt' }, {})).toBe(
+      false
+    )
+    expect(
+      shouldReplaceExistingWithSkippedDocument(
+        { storageKey: 'kb/indexed.txt' },
+        { skippedExistingDisposition: 'replace' }
+      )
+    ).toBe(true)
+  })
+
   it('replaces stale indexed content for an authoritative skip', async () => {
     const { classifyExternalDoc } = await import('@/lib/knowledge/connectors/sync-engine')
 
diff --git a/apps/sim/lib/knowledge/connectors/sync-engine.ts b/apps/sim/lib/knowledge/connectors/sync-engine.ts
index 84d890db819..bdca8b716f0 100644
--- a/apps/sim/lib/knowledge/connectors/sync-engine.ts
+++ b/apps/sim/lib/knowledge/connectors/sync-engine.ts
@@ -454,6 +454,13 @@ type DocClassification =
   | { type: 'unchanged' }
   | { type: 'drop' }
 
+export function shouldReplaceExistingWithSkippedDocument(
+  existing: { storageKey?: string | null },
+  skipped: Pick<ExternalDocument, 'skippedExistingDisposition'>
+): boolean {
+  return existing.storageKey === null || skipped.skippedExistingDisposition === 'replace'
+}
+
 /**
  * Decides what a listed external document becomes during reconciliation.
  *
@@ -487,7 +494,7 @@ export function classifyExternalDoc(
 ): DocClassification {
   if (extDoc.skippedReason) {
     if (!existing) return { type: 'skip' }
-    return existing.storageKey === null || extDoc.skippedExistingDisposition === 'replace'
+    return shouldReplaceExistingWithSkippedDocument(existing, extDoc)
       ? { type: 'skip', existingId: existing.id }
       : { type: 'unchanged' }
   }
@@ -2377,7 +2384,8 @@ export async function executeSync(
                   extDoc: mergeHydratedSkippedDocument(op.extDoc, fullDoc),
                 })
               } else if (op.type === 'update') {
-                if (fullDoc.skippedExistingDisposition === 'replace') {
+                const existing = priorByExternalId.get(op.extDoc.externalId)
+                if (existing && shouldReplaceExistingWithSkippedDocument(existing, fullDoc)) {
                   skipOps.push({
                     type: 'skip',
                     existingId: op.existingId,