diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index 104ef8f..933e21a 100755
--- a/scripts/agent-branch-finish.sh
+++ b/scripts/agent-branch-finish.sh
@@ -508,7 +508,7 @@ is_local_branch_delete_error() {
 
 is_remote_branch_missing_error() {
   local output="$1"
-  if [[ "$output" == *"remote ref does not exist"* ]] || [[ "$output" == *"failed to push some refs"* ]]; then
+  if [[ "$output" == *"remote ref does not exist"* ]]; then
     return 0
   fi
   return 1
@@ -893,8 +893,8 @@ if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
         if is_remote_branch_missing_error "$remote_delete_output"; then
           echo "[agent-branch-finish] Remote branch '${SOURCE_BRANCH}' was already deleted; continuing cleanup." >&2
         else
+          echo "[agent-branch-finish] Warning: remote branch cleanup failed for '${SOURCE_BRANCH}' after merge; continuing local cleanup." >&2
           echo "$remote_delete_output" >&2
-          exit 1
         fi
       fi
     fi
diff --git a/templates/vscode/guardex-active-agents/extension.js b/templates/vscode/guardex-active-agents/extension.js
index d96ae0b..d7fb051 100644
--- a/templates/vscode/guardex-active-agents/extension.js
+++ b/templates/vscode/guardex-active-agents/extension.js
@@ -2395,6 +2395,51 @@ function isPathWithin(parentPath, targetPath) {
   return relativePath === '' || (!relativePath.startsWith('..') && !path.isAbsolute(relativePath));
 }
 
+function normalizeAbsolutePath(value) {
+  return typeof value === 'string' && value.trim() ? path.resolve(value) : '';
+}
+
+function removeDeletedWorktreeWorkspaceFolder(worktreePath) {
+  if (typeof vscode.workspace.updateWorkspaceFolders !== 'function') {
+    return false;
+  }
+
+  const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+  if (!normalizedWorktreePath) {
+    return false;
+  }
+
+  const workspaceFolders = vscode.workspace.workspaceFolders || [];
+  const folderIndex = workspaceFolders.findIndex((folder) => (
+    normalizeAbsolutePath(folder?.uri?.fsPath) === normalizedWorktreePath
+  ));
+  if (folderIndex < 0) {
+    return false;
+  }
+
+  try {
+    return vscode.workspace.updateWorkspaceFolders(folderIndex, 1) === true;
+  } catch (_error) {
+    return false;
+  }
+}
+
+async function closeDeletedWorktreeRepository(worktreePath) {
+  const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+  if (!normalizedWorktreePath || fs.existsSync(normalizedWorktreePath)) {
+    return false;
+  }
+
+  try {
+    await vscode.commands.executeCommand('git.close', vscode.Uri.file(normalizedWorktreePath));
+  } catch (_error) {
+    // The Git extension may have already removed this repository.
+  }
+
+  removeDeletedWorktreeWorkspaceFolder(normalizedWorktreePath);
+  return true;
+}
+
 function localizeChangeForSession(session, change) {
   if (!change?.absolutePath || !isPathWithin(session.worktreePath, change.absolutePath)) {
     return null;
@@ -3434,6 +3479,7 @@ class ActiveAgentsRefreshController {
     this.inspectPanelManager = inspectPanelManager;
     this.refreshTimer = null;
     this.sessionWatchers = new Map();
+    this.closedMissingWorktreeRepositories = new Set();
   }
 
   scheduleRefresh() {
@@ -3458,6 +3504,16 @@ class ActiveAgentsRefreshController {
 
     for (const entry of repoEntries) {
       for (const session of entry.sessions) {
+        const worktreePath = sessionWorktreePath(session);
+        const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+        if (normalizedWorktreePath && !fs.existsSync(normalizedWorktreePath)) {
+          await this.closeMissingWorktreeRepository(normalizedWorktreePath);
+          continue;
+        }
+        if (normalizedWorktreePath) {
+          this.closedMissingWorktreeRepositories.delete(normalizedWorktreePath);
+        }
+
         const sessionKey = resolveSessionWatcherKey(session);
         liveSessionKeys.add(sessionKey);
         if (this.sessionWatchers.has(sessionKey)) {
@@ -3483,6 +3539,16 @@ class ActiveAgentsRefreshController {
     }
   }
 
+  async closeMissingWorktreeRepository(worktreePath) {
+    const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+    if (!normalizedWorktreePath || this.closedMissingWorktreeRepositories.has(normalizedWorktreePath)) {
+      return;
+    }
+
+    this.closedMissingWorktreeRepositories.add(normalizedWorktreePath);
+    await closeDeletedWorktreeRepository(normalizedWorktreePath);
+  }
+
   dispose() {
     if (this.refreshTimer) {
       clearTimeout(this.refreshTimer);
diff --git a/templates/vscode/guardex-active-agents/package.json b/templates/vscode/guardex-active-agents/package.json
index 8c009a2..c725ca6 100644
--- a/templates/vscode/guardex-active-agents/package.json
+++ b/templates/vscode/guardex-active-agents/package.json
@@ -3,7 +3,7 @@
   "displayName": "GitGuardex Active Agents",
   "description": "Shows live Guardex sandbox sessions and repo changes in a dedicated VS Code Active Agents sidebar.",
   "publisher": "Recodee",
-  "version": "0.0.20",
+  "version": "0.0.21",
   "license": "MIT",
   "icon": "icon.png",
   "engines": {
diff --git a/test/vscode-active-agents-session-state.test.js b/test/vscode-active-agents-session-state.test.js
index de76793..4ba6be3 100644
--- a/test/vscode-active-agents-session-state.test.js
+++ b/test/vscode-active-agents-session-state.test.js
@@ -280,6 +280,7 @@ function createMockVscode(tempRoot) {
     fileWatchers: [],
     watchers: [],
     workspaceFolderListeners: [],
+    workspaceFolderUpdates: [],
     configurationUpdates: [],
     workspaceConfigurationValues: new Map(),
   };
@@ -643,6 +644,11 @@ function createMockVscode(tempRoot) {
             }
           });
         },
+        updateWorkspaceFolders(start, deleteCount, ...folders) {
+          registrations.workspaceFolderUpdates.push({ start, deleteCount, folders });
+          this.workspaceFolders.splice(start, deleteCount, ...folders);
+          return true;
+        },
         workspaceFolders: [{ uri: { fsPath: tempRoot } }],
       },
       ConfigurationTarget,
@@ -1507,6 +1513,60 @@ test('active-agents extension registers tree and decoration providers', async ()
   }
 });
 
+test('active-agents extension closes deleted worktree repositories during refresh', async () => {
+  const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), 'guardex-vscode-close-deleted-'));
+  const worktreePath = path.join(tempRoot, '.omx', 'agent-worktrees', 'deleted-task');
+  fs.mkdirSync(worktreePath, { recursive: true });
+  const sessionPath = writeSessionRecord(tempRoot, sessionSchema.buildSessionRecord({
+    repoRoot: tempRoot,
+    branch: 'agent/codex/deleted-task',
+    taskName: 'deleted-task',
+    agentName: 'codex',
+    worktreePath,
+    pid: process.pid,
+    cliName: 'codex',
+  }));
+
+  const { registrations, vscode } = createMockVscode(tempRoot);
+  vscode.workspace.workspaceFolders = [
+    { uri: { fsPath: tempRoot } },
+    { uri: { fsPath: worktreePath } },
+  ];
+  vscode.workspace.findFiles = async () => [{ fsPath: sessionPath }];
+  const extension = loadExtensionWithMockVscode(vscode);
+  const context = { subscriptions: [] };
+
+  extension.activate(context);
+  await flushAsyncWork();
+
+  const gitCloseCalls = () => registrations.executedCommands.filter((entry) => (
+    entry.command === 'git.close'
+  ));
+  assert.equal(gitCloseCalls().length, 0);
+
+  fs.rmSync(worktreePath, { recursive: true, force: true });
+  await registrations.commands.get('gitguardex.activeAgents.refresh')();
+  await flushAsyncWork();
+
+  assert.equal(gitCloseCalls().length, 1);
+  assert.equal(gitCloseCalls()[0].args[0].fsPath, path.resolve(worktreePath));
+  assert.deepEqual(registrations.workspaceFolderUpdates, [
+    { start: 1, deleteCount: 1, folders: [] },
+  ]);
+  assert.deepEqual(
+    vscode.workspace.workspaceFolders.map((folder) => folder.uri.fsPath),
+    [tempRoot],
+  );
+
+  await registrations.commands.get('gitguardex.activeAgents.refresh')();
+  await flushAsyncWork();
+  assert.equal(gitCloseCalls().length, 1);
+
+  for (const subscription of context.subscriptions) {
+    subscription.dispose?.();
+  }
+});
+
 test('active-agents restart command restarts the extension host for this extension only', async () => {
   const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), 'guardex-vscode-restart-command-'));
   const { registrations, vscode } = createMockVscode(tempRoot);
diff --git a/vscode/guardex-active-agents/extension.js b/vscode/guardex-active-agents/extension.js
index d96ae0b..d7fb051 100644
--- a/vscode/guardex-active-agents/extension.js
+++ b/vscode/guardex-active-agents/extension.js
@@ -2395,6 +2395,51 @@ function isPathWithin(parentPath, targetPath) {
   return relativePath === '' || (!relativePath.startsWith('..') && !path.isAbsolute(relativePath));
 }
 
+function normalizeAbsolutePath(value) {
+  return typeof value === 'string' && value.trim() ? path.resolve(value) : '';
+}
+
+function removeDeletedWorktreeWorkspaceFolder(worktreePath) {
+  if (typeof vscode.workspace.updateWorkspaceFolders !== 'function') {
+    return false;
+  }
+
+  const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+  if (!normalizedWorktreePath) {
+    return false;
+  }
+
+  const workspaceFolders = vscode.workspace.workspaceFolders || [];
+  const folderIndex = workspaceFolders.findIndex((folder) => (
+    normalizeAbsolutePath(folder?.uri?.fsPath) === normalizedWorktreePath
+  ));
+  if (folderIndex < 0) {
+    return false;
+  }
+
+  try {
+    return vscode.workspace.updateWorkspaceFolders(folderIndex, 1) === true;
+  } catch (_error) {
+    return false;
+  }
+}
+
+async function closeDeletedWorktreeRepository(worktreePath) {
+  const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+  if (!normalizedWorktreePath || fs.existsSync(normalizedWorktreePath)) {
+    return false;
+  }
+
+  try {
+    await vscode.commands.executeCommand('git.close', vscode.Uri.file(normalizedWorktreePath));
+  } catch (_error) {
+    // The Git extension may have already removed this repository.
+  }
+
+  removeDeletedWorktreeWorkspaceFolder(normalizedWorktreePath);
+  return true;
+}
+
 function localizeChangeForSession(session, change) {
   if (!change?.absolutePath || !isPathWithin(session.worktreePath, change.absolutePath)) {
     return null;
@@ -3434,6 +3479,7 @@ class ActiveAgentsRefreshController {
     this.inspectPanelManager = inspectPanelManager;
     this.refreshTimer = null;
     this.sessionWatchers = new Map();
+    this.closedMissingWorktreeRepositories = new Set();
   }
 
   scheduleRefresh() {
@@ -3458,6 +3504,16 @@ class ActiveAgentsRefreshController {
 
     for (const entry of repoEntries) {
       for (const session of entry.sessions) {
+        const worktreePath = sessionWorktreePath(session);
+        const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+        if (normalizedWorktreePath && !fs.existsSync(normalizedWorktreePath)) {
+          await this.closeMissingWorktreeRepository(normalizedWorktreePath);
+          continue;
+        }
+        if (normalizedWorktreePath) {
+          this.closedMissingWorktreeRepositories.delete(normalizedWorktreePath);
+        }
+
         const sessionKey = resolveSessionWatcherKey(session);
         liveSessionKeys.add(sessionKey);
         if (this.sessionWatchers.has(sessionKey)) {
@@ -3483,6 +3539,16 @@ class ActiveAgentsRefreshController {
     }
   }
 
+  async closeMissingWorktreeRepository(worktreePath) {
+    const normalizedWorktreePath = normalizeAbsolutePath(worktreePath);
+    if (!normalizedWorktreePath || this.closedMissingWorktreeRepositories.has(normalizedWorktreePath)) {
+      return;
+    }
+
+    this.closedMissingWorktreeRepositories.add(normalizedWorktreePath);
+    await closeDeletedWorktreeRepository(normalizedWorktreePath);
+  }
+
   dispose() {
     if (this.refreshTimer) {
       clearTimeout(this.refreshTimer);
diff --git a/vscode/guardex-active-agents/package.json b/vscode/guardex-active-agents/package.json
index 8c009a2..c725ca6 100644
--- a/vscode/guardex-active-agents/package.json
+++ b/vscode/guardex-active-agents/package.json
@@ -3,7 +3,7 @@
   "displayName": "GitGuardex Active Agents",
   "description": "Shows live Guardex sandbox sessions and repo changes in a dedicated VS Code Active Agents sidebar.",
   "publisher": "Recodee",
-  "version": "0.0.20",
+  "version": "0.0.21",
   "license": "MIT",
   "icon": "icon.png",
   "engines": {