fix(knowledge): resurrect atomically on content update, sweep tombstoned docs on connector teardown

Two real gaps found by review, both stemming from the same root
cause: other code paths assumed deletedAt IS NULL means 'the only
real rows' and were never updated for the new tombstone semantics.

- updateDocument's guard required deletedAt IS NULL, so a tombstoned
  document reappearing with CHANGED content failed its content
  update (rejected by the guard) while the separate resurrect step
  still cleared deletedAt regardless — the document became active
  again but kept serving stale pre-tombstone content. Fixed by
  clearing deletedAt as part of the same update statement and
  dropping the guard, so content and resurrection land atomically.
- Both connector-teardown cleanup paths (the ConnectorDeletedException
  handler in sync-engine.ts, and the connector DELETE API route) only
  swept documents with deletedAt IS NULL, so pending-removal documents
  escaped cleanup entirely and were orphaned once their connector was
  gone. Fixed by including tombstoned docs in both sweeps — there's no
  future sync left to confirm or resurrect them once the connector
  itself is deleted.

Author: waleedlatif1

apps/sim/app/api/knowledge/[id]/connectors/[connectorId]/route.ts

@@ -328,16 +328,12 @@ export const DELETE = withRouteHandler(async (request: NextRequest, { params }:
     const { deletedDocs, docCount } = await db.transaction(async (tx) => {
       await tx.execute(sql`SELECT 1 FROM knowledge_connector WHERE id = ${connectorId} FOR UPDATE`)
 
+      // Includes pending-removal (tombstoned) docs — the connector is being
+      // deleted, so there's no future sync left to confirm or resurrect them.
       const docs = await tx
         .select({ id: document.id, fileUrl: document.fileUrl })
         .from(document)
-        .where(
-          and(
-            eq(document.connectorId, connectorId),
-            isNull(document.archivedAt),
-            isNull(document.deletedAt)
-          )
-        )
+        .where(and(eq(document.connectorId, connectorId), isNull(document.archivedAt)))
 
       if (deleteDocuments) {
         const documentIds = docs.map((doc) => doc.id)

apps/sim/lib/knowledge/connectors/sync-engine.ts

@@ -1002,16 +1002,12 @@ export async function executeSync(
       logger.info('Connector deleted during sync, cleaning up', { connectorId })
 
       try {
+        // Includes pending-removal (tombstoned) docs — the connector is gone, so
+        // there's no future sync left to confirm or resurrect them.
         const connectorDocs = await db
           .select({ id: document.id })
           .from(document)
-          .where(
-            and(
-              eq(document.connectorId, connectorId),
-              isNull(document.archivedAt),
-              isNull(document.deletedAt)
-            )
-          )
+          .where(and(eq(document.connectorId, connectorId), isNull(document.archivedAt)))
 
         await hardDeleteDocuments(
           connectorDocs.map((doc) => doc.id),
@@ -1341,14 +1337,13 @@ async function updateDocument(
           ...tagValues,
           processingStatus: 'pending',
           uploadedAt: new Date(),
+          // A tombstoned document reappearing with changed content is resurrected
+          // in the same write as its content update — otherwise reconciliation's
+          // separate resurrect step would clear deletedAt while this update, gated
+          // on deletedAt IS NULL, rejects the row and leaves stale content active.
+          deletedAt: null,
         })
-        .where(
-          and(
-            eq(document.id, existingDocId),
-            isNull(document.archivedAt),
-            isNull(document.deletedAt)
-          )
-        )
+        .where(and(eq(document.id, existingDocId), isNull(document.archivedAt)))
         .returning({ id: document.id })
         .then((rows) => {
           if (rows.length === 0) {