diff --git a/tests/test_check_upstream_updates.py b/tests/test_check_upstream_updates.py
index a78b4c3..3b2705a 100644
--- a/tests/test_check_upstream_updates.py
+++ b/tests/test_check_upstream_updates.py
@@ -131,5 +131,33 @@ class UpstreamRemotePresentTests(UpstreamCheckerRepoFixture):
         self.assertIn("up to date with upstream/master", result.stdout)
 
 
+class UpstreamRefMissingFileTests(UpstreamCheckerRepoFixture):
+    """Simulates upstream renaming/deleting one framework file while the
+    fork still has its own copy: git show then fails, and the checker used
+    to swallow the error and report a clean '[OK]'."""
+
+    def setUp(self):
+        super().setUp()
+        self.add_remote("origin", FORK_URL)
+        self.add_remote("upstream", TEMPLATE_URL)
+
+        # Upstream drops AGENTS.md (rename/delete) in a new commit.
+        subprocess.run(["git", "rm", "-q", "AGENTS.md"], cwd=self.root, check=True, capture_output=True)
+        subprocess.run(["git", "commit", "-qm", "drop AGENTS.md"], cwd=self.root, check=True, capture_output=True)
+        self.materialize_remote_ref("upstream")
+
+        # The fork keeps its own copy locally, so only the upstream side
+        # lacks the file.
+        (self.root / "AGENTS.md").write_text(FRONTMATTER, encoding="utf-8")
+
+    def test_file_missing_upstream_is_reported_instead_of_silent_ok(self):
+        result = self.run_checker()
+
+        self.assertEqual(result.returncode, 0, result.stdout + result.stderr)
+        self.assertIn("AGENTS.md", result.stdout)
+        self.assertNotIn("[OK] All framework files are up to date", result.stdout)
+        self.assertIn("[WARNING]", result.stdout)
+
+
 if __name__ == "__main__":
     unittest.main()
diff --git a/tools/check_upstream_updates.py b/tools/check_upstream_updates.py
index 0c9a1b1..4a734b8 100755
--- a/tools/check_upstream_updates.py
+++ b/tools/check_upstream_updates.py
@@ -113,6 +113,7 @@ def main() -> int:
     
     updates_available = []
     errors = []
+    missing_upstream = []
 
     for rel_path in FRAMEWORK_FILES:
         local_path = ROOT / rel_path
@@ -125,9 +126,16 @@ def main() -> int:
         local_ver = get_framework_version_from_text(local_text)
         
         # Get upstream version
-        rc, upstream_text, _ = run_git(["show", f"{ref}:{rel_path}"])
+        rc, upstream_text, git_err = run_git(["show", f"{ref}:{rel_path}"])
         if rc != 0:
-            # File might not exist upstream yet
+            # A file present locally but missing from the upstream ref means
+            # it was renamed or deleted upstream; any other git failure means
+            # the comparison is incomplete. Either way, never report a clean
+            # '[OK]' while silently skipping the file.
+            if "does not exist" in git_err or "exists on disk, but not in" in git_err:
+                missing_upstream.append(rel_path)
+            else:
+                errors.append(f"Failed to read upstream version of {rel_path}: {git_err.strip()}")
             continue
             
         upstream_ver = get_framework_version_from_text(upstream_text)
@@ -153,6 +161,12 @@ def main() -> int:
             print(f"  - {err}")
         print()
 
+    if missing_upstream:
+        print("Files present locally but missing from the upstream ref (possibly renamed or deleted upstream):")
+        for path in missing_upstream:
+            print(f"  - {path}")
+        print()
+
     if updates_available:
         print("[UPDATE] Upstream updates available for framework methodology files:")
         for up in updates_available:
@@ -162,7 +176,14 @@ def main() -> int:
         print("Review these changes to see if they fit your personalized fork!")
         return 0
     else:
-        print(f"[OK] All framework files are up to date with {ref}!")
+        if errors or missing_upstream:
+            print(
+                f"[WARNING] Framework check incomplete against {ref}: "
+                f"{len(errors)} configuration error(s), {len(missing_upstream)} file(s) missing upstream. "
+                "Review the messages above before assuming you are up to date."
+            )
+        else:
+            print(f"[OK] All framework files are up to date with {ref}!")
         return 0
 
 if __name__ == "__main__":