diff --git a/server/services/brainSyncLog.js b/server/services/brainSyncLog.js
index e3a00ed9f..82016ce90 100644
--- a/server/services/brainSyncLog.js
+++ b/server/services/brainSyncLog.js
@@ -261,6 +261,8 @@ export async function compactLog(minSeq) {
       kept.push({ line, seq: entry.seq });
     }
 
+    if (dropped === 0) return 0;
+
     const newContent = kept.length > 0 ? kept.map(k => k.line).join('\n') + '\n' : '';
     await atomicWrite(SYNC_LOG_FILE, newContent);
 
diff --git a/server/services/brainSyncLog.test.js b/server/services/brainSyncLog.test.js
index 20df7df6c..c7cbfd877 100644
--- a/server/services/brainSyncLog.test.js
+++ b/server/services/brainSyncLog.test.js
@@ -434,5 +434,46 @@ describe('brainSyncLog', () => {
       expect(lastReadStart()).toBe(lineOffset(2));
       expect(result.changes.map(c => c.seq)).toEqual([5]);
     });
+
+    it('keeps exactly the newest entry when compactLog(currentSeq) is called and recovers seq across restarts (#5439)', async () => {
+      for (let i = 0; i < 5; i++) {
+        await appendChange('create', 'people', `p${i}`, { name: `Person ${i}` }, 'inst-1');
+      }
+      expect(getCurrentSeq()).toBe(5);
+
+      // Compact keeping only seq >= 5
+      const dropped = await compactLog(getCurrentSeq());
+      expect(dropped).toBe(4);
+
+      // Verify file on disk has only seq 5
+      const lines = readFileSync(syncLogPath(), 'utf8').trim().split('\n');
+      expect(lines).toHaveLength(1);
+      const parsed = JSON.parse(lines[0]);
+      expect(parsed.seq).toBe(5);
+      expect(parsed.id).toBe('p4');
+
+      // Simulate restart: re-initialize the log
+      await initSyncLog();
+      expect(getCurrentSeq()).toBe(5);
+
+      // Subsequent appends continue monotonic sequence numbers
+      const nextEntry = await appendChange('create', 'people', 'p5', { name: 'Person 5' }, 'inst-1');
+      expect(nextEntry.seq).toBe(6);
+      expect(getCurrentSeq()).toBe(6);
+    });
+
+    it('returns 0 and does not rewrite file when no entries are dropped (#5439)', async () => {
+      for (let i = 0; i < 3; i++) {
+        await appendChange('create', 'people', `p${i}`, { name: `Person ${i}` }, 'inst-1');
+      }
+      const beforeContent = readFileSync(syncLogPath(), 'utf8');
+
+      // Calling compactLog with minSeq <= 1 drops nothing
+      const dropped = await compactLog(1);
+      expect(dropped).toBe(0);
+
+      const afterContent = readFileSync(syncLogPath(), 'utf8');
+      expect(afterContent).toBe(beforeContent);
+    });
   });
 });
diff --git a/server/services/syncOrchestrator.js b/server/services/syncOrchestrator.js
index 5c6f2dcf1..eb3def54b 100644
--- a/server/services/syncOrchestrator.js
+++ b/server/services/syncOrchestrator.js
@@ -874,6 +874,11 @@ export async function syncAllPeers() {
     });
     const minSeq = Math.min(...consumedSeqs);
     await brainSyncLog.compactLog(minSeq);
+  } else if (brainSyncLog.getCurrentSeq() > 0) {
+    // No brain-sync peer will ever pull these entries; a peer added later
+    // converges through the reconcile snapshot (#1077). Keep the last entry so
+    // initSyncLog still recovers the sequence counter across restarts.
+    await brainSyncLog.compactLog(brainSyncLog.getCurrentSeq());
   }
 }
 
diff --git a/server/services/syncOrchestrator.test.js b/server/services/syncOrchestrator.test.js
index 3cce6b4c1..8a6907d49 100644
--- a/server/services/syncOrchestrator.test.js
+++ b/server/services/syncOrchestrator.test.js
@@ -847,6 +847,39 @@ describe('syncOrchestrator', () => {
 
       expect(compactLog).toHaveBeenCalledWith(0);
     });
+
+    it('compacts to getCurrentSeq() when peers are configured but none is brain-enabled (#5439)', async () => {
+      const memoryOnlyPeer = {
+        ...mockPeer,
+        instanceId: 'A',
+        syncCategories: { brain: false, memory: true }
+      };
+      getPeers.mockResolvedValue([memoryOnlyPeer]);
+      readJSONFile.mockImplementation(async () => ({}));
+
+      await syncAllPeers();
+
+      expect(compactLog).toHaveBeenCalledWith(200);
+    });
+
+    it('compacts to getCurrentSeq() when no peers are configured (#5439)', async () => {
+      getPeers.mockResolvedValue([]);
+      readJSONFile.mockImplementation(async () => ({}));
+
+      await syncAllPeers();
+
+      expect(compactLog).toHaveBeenCalledWith(200);
+    });
+
+    it('does not call compactLog when no brain peers exist and getCurrentSeq() is 0 (#5439)', async () => {
+      getCurrentSeq.mockReturnValue(0);
+      getPeers.mockResolvedValue([]);
+      readJSONFile.mockImplementation(async () => ({}));
+
+      await syncAllPeers();
+
+      expect(compactLog).not.toHaveBeenCalled();
+    });
   });
 
   describe('initSyncOrchestrator', () => {