diff --git a/gstack-upgrade/SKILL.md b/gstack-upgrade/SKILL.md
index 9f0f2f7ea..5248dc21d 100644
--- a/gstack-upgrade/SKILL.md
+++ b/gstack-upgrade/SKILL.md
@@ -131,6 +131,7 @@ cd "$INSTALL_DIR"
 STASH_OUTPUT=$(git stash 2>&1)
 git fetch origin
 git reset --hard origin/main
+find "$INSTALL_DIR" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +
 ./setup
 ```
 If `$STASH_OUTPUT` contains "Saved working directory", warn the user: "Note: local changes were stashed. Run `git stash pop` in the skill directory to restore them."
@@ -180,8 +181,9 @@ Tell user: "Removed vendored copy at `$LOCAL_GSTACK` (team mode active — globa
 **If `LOCAL_GSTACK` is non-empty AND `TEAM_MODE` is NOT `true`:** Update it by copying from the freshly-upgraded primary install (same approach as README vendored install):
 ```bash
 mv "$LOCAL_GSTACK" "$LOCAL_GSTACK.bak"
-cp -Rf "$INSTALL_DIR" "$LOCAL_GSTACK"
-rm -rf "$LOCAL_GSTACK/.git"
+mkdir -p "$LOCAL_GSTACK"
+rsync -a --exclude='.git' --exclude='.bak*' "$INSTALL_DIR/" "$LOCAL_GSTACK/"
+find "$LOCAL_GSTACK" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +
 cd "$LOCAL_GSTACK" && ./setup
 rm -rf "$LOCAL_GSTACK.bak"
 ```
diff --git a/gstack-upgrade/SKILL.md.tmpl b/gstack-upgrade/SKILL.md.tmpl
index 5402a1da3..c3b0be3bd 100644
--- a/gstack-upgrade/SKILL.md.tmpl
+++ b/gstack-upgrade/SKILL.md.tmpl
@@ -128,6 +128,7 @@ cd "$INSTALL_DIR"
 STASH_OUTPUT=$(git stash 2>&1)
 git fetch origin
 git reset --hard origin/main
+find "$INSTALL_DIR" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +
 ./setup
 ```
 If `$STASH_OUTPUT` contains "Saved working directory", warn the user: "Note: local changes were stashed. Run `git stash pop` in the skill directory to restore them."
@@ -177,8 +178,9 @@ Tell user: "Removed vendored copy at `$LOCAL_GSTACK` (team mode active — globa
 **If `LOCAL_GSTACK` is non-empty AND `TEAM_MODE` is NOT `true`:** Update it by copying from the freshly-upgraded primary install (same approach as README vendored install):
 ```bash
 mv "$LOCAL_GSTACK" "$LOCAL_GSTACK.bak"
-cp -Rf "$INSTALL_DIR" "$LOCAL_GSTACK"
-rm -rf "$LOCAL_GSTACK/.git"
+mkdir -p "$LOCAL_GSTACK"
+rsync -a --exclude='.git' --exclude='.bak*' "$INSTALL_DIR/" "$LOCAL_GSTACK/"
+find "$LOCAL_GSTACK" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +
 cd "$LOCAL_GSTACK" && ./setup
 rm -rf "$LOCAL_GSTACK.bak"
 ```
diff --git a/test/gen-skill-docs.test.ts b/test/gen-skill-docs.test.ts
index 2fb783ffd..f6a4aa3e1 100644
--- a/test/gen-skill-docs.test.ts
+++ b/test/gen-skill-docs.test.ts
@@ -498,6 +498,13 @@ describe('gen-skill-docs', () => {
     expect(qaOnlyContent).toContain('Phase 6');
   });
 
+  test('gstack-upgrade generated skill excludes backup trees during upgrade sync', () => {
+    const content = fs.readFileSync(path.join(ROOT, 'gstack-upgrade', 'SKILL.md'), 'utf-8');
+    expect(content).toContain(`find "$INSTALL_DIR" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +`);
+    expect(content).toContain(`rsync -a --exclude='.git' --exclude='.bak*' "$INSTALL_DIR/" "$LOCAL_GSTACK/"`);
+    expect(content).toContain(`find "$LOCAL_GSTACK" -maxdepth 1 -mindepth 1 -name '.bak*' -exec rm -rf {} +`);
+  });
+
   test('qa-only has no-fix guardrails', () => {
     const qaOnlyContent = fs.readFileSync(path.join(ROOT, 'qa-only', 'SKILL.md'), 'utf-8');
     expect(qaOnlyContent).toContain('Never fix bugs');