diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index c7081335e..874a9e699 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -6,7 +6,7 @@
  * manages create, enter, detect, and teardown for auto-mode worktrees.
  */
 
-import { existsSync, cpSync, readFileSync, writeFileSync, readdirSync, mkdirSync, realpathSync, utimesSync } from "node:fs";
+import { existsSync, cpSync, readFileSync, writeFileSync, readdirSync, mkdirSync, realpathSync, utimesSync, unlinkSync } from "node:fs";
 import { isAbsolute, join, resolve } from "node:path";
 import { copyWorktreeDb, reconcileWorktreeDb, isDbAvailable } from "./gsd-db.js";
 import { execSync, execFileSync } from "node:child_process";
@@ -560,6 +560,16 @@ export function mergeMilestoneToMain(
   //    when main is already checked out in the project-root worktree, #757)
   const currentBranchAtBase = nativeGetCurrentBranch(originalBasePath_);
   if (currentBranchAtBase !== mainBranch) {
+    // Remove untracked .gsd/ state files that may conflict with the branch
+    // being checked out. These are regenerated by doctor/rebuildState and
+    // are not meaningful in the main working tree — the worktree had the
+    // real state. Without this, `git checkout main` fails with
+    // "Your local changes would be overwritten" (#827).
+    const gsdStateFiles = ["STATE.md", "completed-units.json", "auto.lock"];
+    for (const f of gsdStateFiles) {
+      const p = join(originalBasePath_, ".gsd", f);
+      try { unlinkSync(p); } catch { /* non-fatal — file may not exist */ }
+    }
     nativeCheckoutBranch(originalBasePath_, mainBranch);
   }