diff --git a/src/core/cycle.ts b/src/core/cycle.ts
index ba53ef640..7c756d8cf 100644
--- a/src/core/cycle.ts
+++ b/src/core/cycle.ts
@@ -978,10 +978,17 @@ async function runPhaseSync(
           sourceId: t.sourceId,
           dryRun,
           noPull: !pull,
-          noEmbed: true,                       // embed is a separate phase
-          noExtract: willRunExtractPhase,      // dedupe ONLY when cycle's extract phase will also run.
-                                               // If extract isn't scheduled (e.g. `gbrain dream --phase sync`),
-                                               // sync's inline extract still runs to preserve prior behavior.
+          noEmbed: true,                       // embed is a separate phase (runEmbedCore --stale is brain-wide,
+                                               // so it covers every target here)
+          // Dedupe inline extract ONLY for the target the cycle's extract
+          // phase will actually cover: extract walks brainDir under
+          // cycleSourceId (runPhaseExtract), so slugs synced from OTHER
+          // checkouts are invisible to it — disabling their inline extract
+          // would silently drop link/timeline extraction for every
+          // non-brainDir source. If extract isn't scheduled at all (e.g.
+          // `gbrain dream --phase sync`), inline extract runs everywhere
+          // to preserve prior behavior.
+          noExtract: willRunExtractPhase && t.repoPath === brainDir,
         });
         synced++;
         added += result.added;
diff --git a/src/core/import-file.ts b/src/core/import-file.ts
index fda3d4a28..7f58f063e 100644
--- a/src/core/import-file.ts
+++ b/src/core/import-file.ts
@@ -1078,10 +1078,17 @@ export async function importCodeFile(
   // previously-imported file BECAME empty, delete the stale page (chunks
   // cascade) so it doesn't ghost in search — mirrors the markdown importer's
   // empty-content branch, which deletes stale chunks.
+  //
+  // NO `error` on the result: sync treats skipped-with-error as a parse
+  // failure (sync.ts pushes it into failedFiles → applySyncFailureGate
+  // BLOCKS last_commit on fresh failures). Empty files are benign and
+  // common (`__init__.py`, barrel stubs) — they must skip like the
+  // content-hash short-circuit (banked/checkpointed, never ledgered),
+  // not block the bookmark.
   if (byteLength === 0) {
     const stale = await engine.getPage(slug, txOpts);
     if (stale) await engine.deletePage(slug, txOpts);
-    return { slug, status: 'skipped', chunks: 0, error: 'empty code file' };
+    return { slug, status: 'skipped', chunks: 0 };
   }
 
   // Vendor-neutral guardrail seam (observe-only, fail-open). Runs AFTER the
diff --git a/test/core/cycle.serial.test.ts b/test/core/cycle.serial.test.ts
index 0bdc90927..4a7201713 100644
--- a/test/core/cycle.serial.test.ts
+++ b/test/core/cycle.serial.test.ts
@@ -662,6 +662,22 @@ describe('runCycle — multi-source sync (#1079)', () => {
     expect(syncCalls.map(c => c.sourceId)).toEqual(['wiki', undefined]);
   });
 
+  test('inline extract stays ON for non-brainDir targets when extract phase is scheduled', async () => {
+    // The cycle's extract phase walks brainDir only (runPhaseExtract), so
+    // dedupe (noExtract: true) is only valid for the brainDir target.
+    // Other sources' checkouts are invisible to the extract phase — their
+    // sync must keep inline extract or links/timeline are never extracted.
+    await (sharedEngine as any).db.query(
+      `INSERT INTO sources (id, name, local_path) VALUES
+        ('wiki', 'wiki', '/tmp/brain-1079-i'),
+        ('code', 'code', '/tmp/brain-1079-j')`,
+    );
+    await runCycle(sharedEngine, { brainDir: '/tmp/brain-1079-i', phases: ['sync', 'extract'] });
+    const byId = new Map(syncCalls.map(c => [c.sourceId, c.noExtract]));
+    expect(byId.get('wiki')).toBe(true);  // covered by the extract phase — dedupe
+    expect(byId.get('code')).toBe(false); // NOT covered — inline extract must run
+  });
+
   test('explicit --source keeps the cycle single-source (#1503)', async () => {
     await (sharedEngine as any).db.query(
       `INSERT INTO sources (id, name, local_path) VALUES
diff --git a/test/import-empty-code-file.test.ts b/test/import-empty-code-file.test.ts
index 2c7c5950d..dae8f872a 100644
--- a/test/import-empty-code-file.test.ts
+++ b/test/import-empty-code-file.test.ts
@@ -5,7 +5,7 @@
  * compiled_truth, which then failed every subsequent `gbrain reindex-code`
  * pass with `missing compiled_truth`. Empty files are legitimate in real
  * repos (stub/placeholder files committed during refactors); the importer
- * skips them the same way it skips files over MAX_FILE_SIZE — and when a
+ * skips them the same way it skips unchanged content (benign, no error) — and when a
  * previously-imported file BECOMES empty, the stale page is deleted (chunks
  * cascade) instead of ghosting in search, mirroring the markdown importer's
  * empty-content branch.
@@ -33,7 +33,11 @@ describe('importCodeFile — empty file guard (#840)', () => {
 
     expect(result.status).toBe('skipped');
     expect(result.chunks).toBe(0);
-    expect(result.error).toBe('empty code file');
+    // NO error on the result: sync treats skipped-with-error as a parse
+    // failure and applySyncFailureGate would BLOCK last_commit on any repo
+    // containing an empty file. Empty files skip like the content-hash
+    // short-circuit — benign, banked, never ledgered.
+    expect(result.error).toBeUndefined();
 
     // The skip must short-circuit before any page row is written, otherwise
     // reindex-code will still trip on the missing compiled_truth.
@@ -48,7 +52,7 @@ describe('importCodeFile — empty file guard (#840)', () => {
 
     const second = await importCodeFile(engine, 'src/becomes-empty.ts', '', { noEmbed: true });
     expect(second.status).toBe('skipped');
-    expect(second.error).toBe('empty code file');
+    expect(second.error).toBeUndefined(); // benign skip — must not enter the sync failure ledger
 
     // Stale page (and its chunks, via FK cascade) must be gone.
     expect(await engine.getPage(first.slug)).toBeNull();