diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index d2420257f..29cab5b97 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -770,6 +770,9 @@ export function syncWorktreeStateBack(
       .map((d) => d.name);
 
     for (const mid of wtMilestones) {
+      // Skip the current milestone being merged — its files are already in the
+      // milestone branch and would conflict with the squash merge (#3641).
+      if (mid === milestoneId) continue;
       syncMilestoneDir(wtGsd, mainGsd, mid, synced);
     }
   } catch (err) {
diff --git a/src/resources/extensions/gsd/tests/sync-worktree-skip-current.test.ts b/src/resources/extensions/gsd/tests/sync-worktree-skip-current.test.ts
new file mode 100644
index 000000000..9b0070cb1
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/sync-worktree-skip-current.test.ts
@@ -0,0 +1,65 @@
+/**
+ * Regression test for #3641 — syncWorktreeStateBack skips current milestone
+ *
+ * When syncing worktree state back to main, the current milestone being
+ * merged should be skipped. Its files are already in the milestone branch
+ * and copying them back would conflict with the squash merge.
+ *
+ * The fix adds a `mid === milestoneId` skip guard inside the milestone
+ * iteration loop in syncWorktreeStateBack.
+ */
+
+import { describe, it } from 'node:test'
+import assert from 'node:assert/strict'
+import { readFileSync } from 'node:fs'
+import { resolve } from 'node:path'
+
+const src = readFileSync(
+  resolve(process.cwd(), 'src', 'resources', 'extensions', 'gsd', 'auto-worktree.ts'),
+  'utf-8',
+)
+
+describe('syncWorktreeStateBack skips current milestone (#3641)', () => {
+  it('syncWorktreeStateBack function exists', () => {
+    assert.ok(
+      src.includes('function syncWorktreeStateBack('),
+      'syncWorktreeStateBack function must be defined',
+    )
+  })
+
+  it('mid === milestoneId skip guard exists in the milestone loop', () => {
+    // Find syncWorktreeStateBack
+    const fnStart = src.indexOf('function syncWorktreeStateBack(')
+    assert.ok(fnStart !== -1)
+
+    // Get a reasonable portion of the function
+    const fnBlock = src.slice(fnStart, fnStart + 3000)
+
+    // Find the for loop iterating milestones
+    const loopIdx = fnBlock.indexOf('for (const mid of wtMilestones)')
+    assert.ok(loopIdx !== -1, 'milestone iteration loop must exist')
+
+    // After the loop, there should be the skip guard
+    const loopBody = fnBlock.slice(loopIdx, loopIdx + 300)
+    assert.ok(
+      loopBody.includes('mid === milestoneId'),
+      'mid === milestoneId skip guard must exist inside the milestone loop',
+    )
+    assert.ok(
+      loopBody.includes('continue'),
+      'skip guard must use continue to skip the current milestone',
+    )
+  })
+
+  it('syncMilestoneDir is still called for non-current milestones', () => {
+    const fnStart = src.indexOf('function syncWorktreeStateBack(')
+    assert.ok(fnStart !== -1)
+
+    const fnBlock = src.slice(fnStart, fnStart + 3000)
+
+    assert.ok(
+      fnBlock.includes('syncMilestoneDir('),
+      'syncMilestoneDir must still be called for other milestones',
+    )
+  })
+})
diff --git a/src/resources/extensions/gsd/tests/worktree-sync-milestones.test.ts b/src/resources/extensions/gsd/tests/worktree-sync-milestones.test.ts
index f50d9df7b..57ebe3740 100644
--- a/src/resources/extensions/gsd/tests/worktree-sync-milestones.test.ts
+++ b/src/resources/extensions/gsd/tests/worktree-sync-milestones.test.ts
@@ -221,7 +221,8 @@ describe('worktree-sync-milestones', async () => {
 
     try {
       // Build worktree milestone structure with slice-level and task-level files
-      const wtSliceDir = join(wtBase, '.gsd', 'milestones', 'M001', 'slices', 'S01');
+      // Use M002 as the milestone to sync, M001 as the "current" being merged (skipped)
+      const wtSliceDir = join(wtBase, '.gsd', 'milestones', 'M002', 'slices', 'S01');
       const wtTasksDir = join(wtSliceDir, 'tasks');
       mkdirSync(wtTasksDir, { recursive: true });
       writeFileSync(join(wtSliceDir, 'S01-SUMMARY.md'), '# S01 Summary');
@@ -229,11 +230,12 @@ describe('worktree-sync-milestones', async () => {
       writeFileSync(join(wtTasksDir, 'T02-SUMMARY.md'), '# T02 Summary');
 
       // Main project root starts with only the milestone directory (no slices yet)
-      mkdirSync(join(mainBase, '.gsd', 'milestones', 'M001'), { recursive: true });
+      mkdirSync(join(mainBase, '.gsd', 'milestones', 'M002'), { recursive: true });
 
+      // Pass M001 as milestoneId (the one being merged/skipped), M002 should still sync
       const { synced } = syncWorktreeStateBack(mainBase, wtBase, 'M001');
 
-      const mainSliceDir = join(mainBase, '.gsd', 'milestones', 'M001', 'slices', 'S01');
+      const mainSliceDir = join(mainBase, '.gsd', 'milestones', 'M002', 'slices', 'S01');
       const mainTasksDir = join(mainSliceDir, 'tasks');
 
       assert.ok(
@@ -341,16 +343,16 @@ describe('worktree-sync-milestones', async () => {
         'M002 missing in main before sync',
       );
 
-      // Sync with milestoneId = M001 (the current milestone)
+      // Sync with milestoneId = M001 (the current milestone being merged — skipped)
       const { synced } = syncWorktreeStateBack(mainBase, wtBase, 'M001');
 
-      // M001 should be synced (current milestone — always synced)
+      // M001 should be SKIPPED (current milestone being merged — #3641)
       assert.ok(
-        existsSync(join(mainBase, '.gsd', 'milestones', 'M001', 'M001-SUMMARY.md')),
-        'M001 SUMMARY synced to main',
+        !existsSync(join(mainBase, '.gsd', 'milestones', 'M001', 'M001-SUMMARY.md')),
+        'M001 SUMMARY NOT synced (current milestone skipped to prevent merge conflicts)',
       );
 
-      // M002 should ALSO be synced (next milestone — the fix)
+      // M002 should be synced (other milestone — not skipped)
       assert.ok(
         existsSync(join(mainBase, '.gsd', 'milestones', 'M002-abc123', 'M002-abc123-CONTEXT.md')),
         'M002 CONTEXT synced to main (next-milestone fix)',
@@ -407,20 +409,17 @@ describe('worktree-sync-milestones', async () => {
       writeFileSync(join(wtBase, '.gsd', 'REQUIREMENTS.md'), '# Requirements\n## R001-R089\n## R090 — SCIM\n## R091 — WebAuthn');
       writeFileSync(join(wtBase, '.gsd', 'PROJECT.md'), '# Project\nMilestones: M001-M007');
 
-      // Sync with milestoneId = M006 (the completing milestone)
+      // Sync with milestoneId = M006 (the completing milestone — skipped by sync)
       const { synced } = syncWorktreeStateBack(mainBase, wtBase, 'M006-589wvh');
 
-      // Verify M006 artifacts synced
+      // M006 is the current milestone being merged — it should be SKIPPED (#3641)
+      // Its files are already in the milestone branch and would conflict with squash merge.
       assert.ok(
-        existsSync(join(mainBase, '.gsd', 'milestones', 'M006-589wvh', 'M006-589wvh-SUMMARY.md')),
-        'M006 SUMMARY synced',
-      );
-      assert.ok(
-        existsSync(join(mainBase, '.gsd', 'milestones', 'M006-589wvh', 'slices', 'S01', 'S01-SUMMARY.md')),
-        'M006 S01 SUMMARY synced',
+        !existsSync(join(mainBase, '.gsd', 'milestones', 'M006-589wvh', 'M006-589wvh-SUMMARY.md')),
+        'M006 SUMMARY NOT synced (current milestone skipped)',
       );
 
-      // Verify M007 artifacts synced (the critical fix)
+      // Verify M007 artifacts synced (the critical fix — other milestones still sync)
       assert.ok(
         existsSync(join(mainBase, '.gsd', 'milestones', 'M007-wortc8', 'M007-wortc8-CONTEXT.md')),
         'M007 CONTEXT synced to main (next-milestone)',
diff --git a/src/resources/extensions/gsd/tests/worktree-sync-tasks.test.ts b/src/resources/extensions/gsd/tests/worktree-sync-tasks.test.ts
index 43d57c59e..65717415c 100644
--- a/src/resources/extensions/gsd/tests/worktree-sync-tasks.test.ts
+++ b/src/resources/extensions/gsd/tests/worktree-sync-tasks.test.ts
@@ -47,7 +47,8 @@ function writeFile(dir: string, relativePath: string, content: string): void {
 test("syncWorktreeStateBack copies task summaries from tasks/ subdirectory (#1678)", () => {
   const mainBase = makeTempDir("main");
   const wtBase = makeTempDir("wt");
-  const mid = "M001";
+  const currentMid = "M000"; // milestone being merged (skipped by sync)
+  const mid = "M001";        // other milestone that should be synced
 
   try {
     // Set up worktree with milestone, slice, and task files
@@ -64,8 +65,8 @@ test("syncWorktreeStateBack copies task summaries from tasks/ subdirectory (#167
     // Set up main with empty .gsd
     mkdirSync(join(mainBase, ".gsd"), { recursive: true });
 
-    // Run sync
-    const result = syncWorktreeStateBack(mainBase, wtBase, mid);
+    // Run sync — currentMid is skipped, mid (M001) should be synced
+    const result = syncWorktreeStateBack(mainBase, wtBase, currentMid);
 
     // Verify milestone-level files synced
     assert.ok(
@@ -126,7 +127,8 @@ test("syncWorktreeStateBack copies task summaries from tasks/ subdirectory (#167
 test("syncWorktreeStateBack handles multiple slices with tasks (#1678)", () => {
   const mainBase = makeTempDir("main");
   const wtBase = makeTempDir("wt");
-  const mid = "M002";
+  const currentMid = "M000"; // milestone being merged (skipped)
+  const mid = "M002";        // other milestone that should be synced
 
   try {
     // Set up two slices with tasks
@@ -139,7 +141,7 @@ test("syncWorktreeStateBack handles multiple slices with tasks (#1678)", () => {
 
     mkdirSync(join(mainBase, ".gsd"), { recursive: true });
 
-    const result = syncWorktreeStateBack(mainBase, wtBase, mid);
+    const result = syncWorktreeStateBack(mainBase, wtBase, currentMid);
 
     // All task summaries from both slices should be synced
     assert.ok(existsSync(join(mainBase, `.gsd/milestones/${mid}/slices/S01/tasks/T01-SUMMARY.md`)));
@@ -160,7 +162,8 @@ test("syncWorktreeStateBack handles multiple slices with tasks (#1678)", () => {
 test("syncWorktreeStateBack handles slices without tasks/ directory", () => {
   const mainBase = makeTempDir("main");
   const wtBase = makeTempDir("wt");
-  const mid = "M003";
+  const currentMid = "M000"; // milestone being merged (skipped)
+  const mid = "M003";        // other milestone that should be synced
 
   try {
     // Slice with no tasks/ subdirectory (legitimate case: pre-planning)
@@ -168,7 +171,7 @@ test("syncWorktreeStateBack handles slices without tasks/ directory", () => {
 
     mkdirSync(join(mainBase, ".gsd"), { recursive: true });
 
-    const result = syncWorktreeStateBack(mainBase, wtBase, mid);
+    const result = syncWorktreeStateBack(mainBase, wtBase, currentMid);
 
     // Should sync the slice file without errors
     assert.ok(existsSync(join(mainBase, `.gsd/milestones/${mid}/slices/S01/S01-RESEARCH.md`)));
@@ -183,7 +186,8 @@ test("syncWorktreeStateBack handles slices without tasks/ directory", () => {
 test("syncWorktreeStateBack ignores non-md files in tasks/", () => {
   const mainBase = makeTempDir("main");
   const wtBase = makeTempDir("wt");
-  const mid = "M004";
+  const currentMid = "M000"; // milestone being merged (skipped)
+  const mid = "M004";        // other milestone that should be synced
 
   try {
     writeFile(wtBase, `.gsd/milestones/${mid}/slices/S01/S01-PLAN.md`, "# Plan\n");
@@ -194,7 +198,7 @@ test("syncWorktreeStateBack ignores non-md files in tasks/", () => {
 
     mkdirSync(join(mainBase, ".gsd"), { recursive: true });
 
-    const result = syncWorktreeStateBack(mainBase, wtBase, mid);
+    const result = syncWorktreeStateBack(mainBase, wtBase, currentMid);
 
     // Only .md files should be synced
     assert.ok(existsSync(join(mainBase, `.gsd/milestones/${mid}/slices/S01/tasks/T01-SUMMARY.md`)));