diff --git a/apps/web/src/components/LegacySidebar.tsx b/apps/web/src/components/LegacySidebar.tsx
index cb3484e097f8f..e8993ddf1d449 100644
--- a/apps/web/src/components/LegacySidebar.tsx
+++ b/apps/web/src/components/LegacySidebar.tsx
@@ -104,6 +104,8 @@ import {
   useOrchestrationCommand,
 } from "../state/use-orchestration-command";
 import { previewEnvironment } from "../state/preview";
+import { vcsEnvironment } from "../state/vcs";
+import { useEnvironmentQuery } from "../state/query";
 import { readEnvironmentScope, useEnvironmentScope } from "../state/session";
 import {
   legacyProjectCwdPreferenceKey,
@@ -198,9 +200,11 @@ import {
   orderItemsByPreferredIds,
   shouldClearThreadSelectionOnMouseDown,
   sortProjectsForSidebar,
+  useRetainedValue,
   useSidebarRowSubscriptionLease,
   useThreadJumpHintVisibility,
   ThreadStatusPill,
+  withoutRemovedCheckout,
 } from "./Sidebar.logic";
 import { sortThreads } from "../lib/threadSort";
 import { SidebarChromeFooter, SidebarChromeHeader } from "./sidebar/SidebarChrome";
@@ -461,6 +465,19 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
     thread.pullRequests,
     thread.branchPullRequest,
   );
+  const gitStatus = useEnvironmentQuery(
+    leaseLiveStatus && thread.worktreePath !== null
+      ? vcsEnvironment.status({
+          environmentId: thread.environmentId,
+          input: { cwd: thread.worktreePath, includeRemote: false },
+        })
+      : null,
+  );
+  const visibleGitStatus = useRetainedValue(
+    JSON.stringify([thread.environmentId, thread.worktreePath]),
+    gitStatus.data,
+  );
+  const checkoutThread = withoutRemovedCheckout(thread, visibleGitStatus);
   const pr = linkedPullRequestStatus?.pr ?? null;
   const supportsMultiplePullRequests = useSupportsMultiplePullRequests(thread.environmentId);
   // Hooks must precede this ref's plain uses for the compiler to cache it.
@@ -779,7 +796,7 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
               </TooltipPopup>
             </Tooltip>
           )}
-          <ThreadWorktreeIndicator thread={thread} />
+          <ThreadWorktreeIndicator thread={checkoutThread} />
           <ThreadTerminalStatusButton
             threadRef={threadRef}
             terminalIds={runningTerminalIds}
diff --git a/apps/web/src/components/Sidebar.logic.ts b/apps/web/src/components/Sidebar.logic.ts
index f2ff8d22e6a89..0b55121a6d922 100644
--- a/apps/web/src/components/Sidebar.logic.ts
+++ b/apps/web/src/components/Sidebar.logic.ts
@@ -108,6 +108,13 @@ export function useRetainedValue<T>(key: string | null, value: T | null): T | nu
   return key !== null && retained?.key === key ? retained.value : null;
 }
 
+// A known non-repository cwd means the stored checkout was removed; unknown status keeps it.
+export function withoutRemovedCheckout<
+  T extends { branch: string | null; worktreePath: string | null },
+>(thread: T, gitStatus: { readonly isRepo: boolean } | null): T {
+  return gitStatus?.isRepo === false ? { ...thread, branch: null, worktreePath: null } : thread;
+}
+
 // Sortable owns drag transforms; replaying committed order would animate drops twice.
 export const animateSidebarLayoutChanges: AnimateLayoutChanges = (args) =>
   args.isSorting ? defaultAnimateLayoutChanges(args) : false;
diff --git a/apps/web/src/components/sidebar/SidebarThreadRow.tsx b/apps/web/src/components/sidebar/SidebarThreadRow.tsx
index c2393f3fe9b7b..f6bb5d6fa9331 100644
--- a/apps/web/src/components/sidebar/SidebarThreadRow.tsx
+++ b/apps/web/src/components/sidebar/SidebarThreadRow.tsx
@@ -83,6 +83,7 @@ import {
   shouldRecedeSidebarThread,
   resolveWorkingStartedAt,
   useRetainedValue,
+  withoutRemovedCheckout,
   useSidebarRowSubscriptionLease,
 } from "../Sidebar.logic";
 import { resolveLocalCheckoutBranchMismatch } from "../BranchToolbar.logic";
@@ -629,6 +630,7 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
     JSON.stringify([thread.environmentId, gitCwd]),
     gitStatus.data,
   );
+  const checkoutThread = withoutRemovedCheckout(thread, visibleGitStatus);
   const pr = linkedPullRequestStatus?.pr ?? null;
   const supportsMultiplePullRequests = useSupportsMultiplePullRequests(thread.environmentId);
   const currentLinkedPr = supportsMultiplePullRequests
@@ -710,9 +712,9 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
   const isWokeStatus = topStatus?.icon === "woke";
 
   const branchMismatch = resolveLocalCheckoutBranchMismatch({
-    effectiveEnvMode: thread.worktreePath === null ? "local" : "worktree",
-    activeWorktreePath: thread.worktreePath,
-    activeThreadBranch: thread.branch,
+    effectiveEnvMode: checkoutThread.worktreePath === null ? "local" : "worktree",
+    activeWorktreePath: checkoutThread.worktreePath,
+    activeThreadBranch: checkoutThread.branch,
     currentGitBranch: visibleGitStatus?.refName ?? null,
   });
   const prStatus = prStatusIndicator(pr, linkedPullRequestStatus?.sourceControlProvider);
@@ -730,11 +732,11 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
     : thread.modelSelection.model;
 
   const isRemote = thread.environmentId !== props.currentEnvironmentId;
-  const showsScratchMachine = !thread.branch && props.scratchMachineLabel !== null;
+  const showsScratchMachine = !checkoutThread.branch && props.scratchMachineLabel !== null;
 
   const detailsTooltip = (
     <SidebarThreadTooltip
-      thread={thread}
+      thread={checkoutThread}
       project={props.project}
       projectDisplayName={props.projectDisplayName}
       environmentLabel={props.environmentLabel}
@@ -1451,11 +1453,11 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: SidebarThreadRowP
               ) : null}
             </div>
             <div className="mt-0.5 flex min-w-0 items-center gap-1.5 text-secondary-label text-xs">
-              {thread.branch ? (
+              {checkoutThread.branch ? (
                 <>
-                  <ThreadWorktreeIndicator thread={thread} />
+                  <ThreadWorktreeIndicator thread={checkoutThread} />
                   <span className="flex min-w-0 flex-1 text-muted-foreground/40 redesign:text-inherit">
-                    <MiddleTruncate value={thread.branch} showTitle={false} />
+                    <MiddleTruncate value={checkoutThread.branch} showTitle={false} />
                   </span>
                 </>
               ) : showsScratchMachine ? (
@@ -1563,10 +1565,11 @@ export const SidebarSearchResultRow = memo(function SidebarSearchResultRow(props
     JSON.stringify([thread.environmentId, gitCwd]),
     gitStatus.data,
   );
+  const checkoutThread = withoutRemovedCheckout(thread, visibleGitStatus);
   const branchMismatch = resolveLocalCheckoutBranchMismatch({
-    effectiveEnvMode: thread.worktreePath === null ? "local" : "worktree",
-    activeWorktreePath: thread.worktreePath,
-    activeThreadBranch: thread.branch,
+    effectiveEnvMode: checkoutThread.worktreePath === null ? "local" : "worktree",
+    activeWorktreePath: checkoutThread.worktreePath,
+    activeThreadBranch: checkoutThread.branch,
     currentGitBranch: visibleGitStatus?.refName ?? null,
   });
   const modelInstanceId = thread.runtime?.providerInstanceId ?? thread.modelSelection.instanceId;
@@ -1679,7 +1682,7 @@ export const SidebarSearchResultRow = memo(function SidebarSearchResultRow(props
           </span>
         </TooltipTrigger>
         <SidebarThreadTooltip
-          thread={thread}
+          thread={checkoutThread}
           project={props.project}
           projectDisplayName={props.projectDisplayName}
           environmentLabel={props.environmentLabel}