diff --git a/packages/kilo-vscode/src/agent-manager/AgentManagerProvider.ts b/packages/kilo-vscode/src/agent-manager/AgentManagerProvider.ts
index ba9c1911b7e..51548eb1be7 100644
--- a/packages/kilo-vscode/src/agent-manager/AgentManagerProvider.ts
+++ b/packages/kilo-vscode/src/agent-manager/AgentManagerProvider.ts
@@ -43,6 +43,8 @@ export class AgentManagerProvider implements vscode.Disposable {
   private diffInterval: ReturnType<typeof setInterval> | undefined
   private diffSessionId: string | undefined
   private lastDiffHash: string | undefined
+  private validationInterval: ReturnType<typeof setInterval> | undefined
+  private validating = false
   private statsPoller: WorktreeStatsPoller
   private cachedDiffTarget: { directory: string; baseBranch: string } | undefined
 
@@ -107,6 +109,7 @@ export class AgentManagerProvider implements vscode.Disposable {
 
     this.panel.onDidDispose(() => {
       this.log("Panel disposed")
+      this.stopWorktreeValidation()
       this.statsPoller.stop()
       this.stopDiffPolling()
       this.provider?.dispose()
@@ -131,7 +134,12 @@ export class AgentManagerProvider implements vscode.Disposable {
 
     // Validate worktree directories still exist (handles manual deletion)
     const root = this.getWorkspaceRoot()
-    if (root) await state.validate(root)
+    if (root) {
+      const orphaned = await state.validate(root)
+      for (const s of orphaned) {
+        this.provider?.clearSessionDirectory(s.id)
+      }
+    }
 
     // Register all worktree sessions with KiloProvider
     for (const worktree of state.getWorktrees()) {
@@ -148,6 +156,10 @@ export class AgentManagerProvider implements vscode.Disposable {
     if (state.getSessions().length > 0) {
       this.provider?.refreshSessions()
     }
+
+    // Poll for externally deleted worktrees while the panel is open.
+    // Guard against panel being disposed while initializeState() was awaiting.
+    if (this.panel) this.startWorktreeValidation()
   }
 
   // ---------------------------------------------------------------------------
@@ -1486,6 +1498,52 @@ export class AgentManagerProvider implements vscode.Disposable {
     this.cachedDiffTarget = undefined
   }
 
+  // ---------------------------------------------------------------------------
+  // Worktree validation polling
+  // ---------------------------------------------------------------------------
+
+  private startWorktreeValidation(): void {
+    this.stopWorktreeValidation()
+    this.validationInterval = setInterval(() => {
+      void this.validateWorktrees()
+    }, 10_000)
+  }
+
+  private stopWorktreeValidation(): void {
+    if (this.validationInterval) {
+      clearInterval(this.validationInterval)
+      this.validationInterval = undefined
+    }
+  }
+
+  private async validateWorktrees(): Promise<void> {
+    if (this.validating) return
+    this.validating = true
+    try {
+      const state = this.getStateManager()
+      const root = this.getWorkspaceRoot()
+      if (!state || !root) return
+
+      const orphaned = await state.validate(root)
+      if (orphaned.length === 0) return
+
+      for (const s of orphaned) {
+        this.provider?.clearSessionDirectory(s.id)
+      }
+
+      // Stop diff polling if it targets an orphaned session
+      if (this.diffSessionId && orphaned.some((s) => s.id === this.diffSessionId)) {
+        this.stopDiffPolling()
+      }
+
+      this.pushState()
+    } catch (error) {
+      this.log("Worktree validation failed:", error)
+    } finally {
+      this.validating = false
+    }
+  }
+
   private postToWebview(message: Record<string, unknown>): void {
     if (this.panel?.webview) void this.panel.webview.postMessage(message)
   }
@@ -1526,6 +1584,7 @@ export class AgentManagerProvider implements vscode.Disposable {
   }
 
   public dispose(): void {
+    this.stopWorktreeValidation()
     this.stopDiffPolling()
     this.statsPoller.stop()
     this.terminalManager.dispose()
diff --git a/packages/kilo-vscode/src/agent-manager/WorktreeStateManager.ts b/packages/kilo-vscode/src/agent-manager/WorktreeStateManager.ts
index 9b135fb07b2..d2cc67703e6 100644
--- a/packages/kilo-vscode/src/agent-manager/WorktreeStateManager.ts
+++ b/packages/kilo-vscode/src/agent-manager/WorktreeStateManager.ts
@@ -280,23 +280,26 @@ export class WorktreeStateManager {
     }
   }
 
-  /** Remove worktrees whose directories no longer exist on disk. */
-  async validate(root: string): Promise<void> {
-    let changed = false
+  /** Remove worktrees whose directories no longer exist on disk. Returns orphaned sessions. */
+  async validate(root: string): Promise<ManagedSession[]> {
+    const orphaned: ManagedSession[] = []
     for (const wt of [...this.worktrees.values()]) {
       const resolved = path.isAbsolute(wt.path) ? wt.path : path.join(root, wt.path)
       if (!fs.existsSync(resolved)) {
         this.log(`Worktree ${wt.id} directory missing (${resolved}), removing`)
-        this.removeWorktree(wt.id)
-        changed = true
+        orphaned.push(...this.removeWorktree(wt.id))
       }
     }
-    if (changed) await this.save()
+    // removeWorktree() already queues a save per call — just wait for completion
+    if (orphaned.length > 0) await this.flush()
+    return orphaned
   }
 
-  /** Wait for any in-flight save to complete without triggering a new one. */
+  /** Wait for all in-flight and queued saves to complete without triggering a new one. */
   async flush(): Promise<void> {
-    if (this.saving) await this.saving
+    while (this.saving || this.pendingSave) {
+      await (this.saving ?? Promise.resolve())
+    }
   }
 
   async save(): Promise<void> {