Update src/specify_cli/__init__.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: mbachorik

src/specify_cli/__init__.py

@@ -2799,13 +2799,53 @@ def extension_update(
                             f"Extension ID mismatch: expected '{extension_id}', got '{zip_extension_id}'"
                         )
 
-                    # 7. Remove old extension (handles command file cleanup and registry removal)
+                    # 7. Backup existing config files (if any) before removal
+                    config_backup_dir = None
+                    if backup_registry_entry:
+                        existing_path = backup_registry_entry.get("path")
+                        if existing_path:
+                            existing_install_dir = Path(existing_path)
+                            if existing_install_dir.is_dir():
+                                # Create a temporary directory to hold backed-up config files
+                                config_backup_dir = Path(
+                                    tempfile.mkdtemp(prefix="speckit-ext-config-")
+                                )
+                                for cfg_file in existing_install_dir.glob("*-config*.yml"):
+                                    try:
+                                        shutil.copy2(cfg_file, config_backup_dir / cfg_file.name)
+                                    except OSError:
+                                        # Best-effort backup; skip files that cannot be copied
+                                        pass
+
+                    # 8. Remove old extension (handles command file cleanup and registry removal)
                     manager.remove(extension_id, keep_config=True)
 
-                    # 8. Install new version
+                    # 9. Install new version
                     _ = manager.install_from_zip(zip_path, speckit_version)
 
-                    # 9. Restore metadata from backup (installed_at, enabled state)
+                    # 10. Restore backed-up config files into the new install directory (if any)
+                    if config_backup_dir is not None:
+                        new_registry_entry = manager.registry.get(extension_id)
+                        new_install_dir = None
+                        if new_registry_entry is not None:
+                            new_path = new_registry_entry.get("path")
+                            if new_path:
+                                new_install_dir = Path(new_path)
+                        if new_install_dir is not None and new_install_dir.is_dir():
+                            for cfg_file in config_backup_dir.glob("*-config*.yml"):
+                                try:
+                                    shutil.copy2(cfg_file, new_install_dir / cfg_file.name)
+                                except OSError:
+                                    # Best-effort restore; skip files that cannot be copied
+                                    pass
+                        # Clean up the temporary backup directory
+                        try:
+                            shutil.rmtree(config_backup_dir, ignore_errors=True)
+                        except OSError:
+                            # Ignore cleanup errors; they do not affect functionality
+                            pass
+
+                    # 11. Restore metadata from backup (installed_at, enabled state)
                     if backup_registry_entry:
                         # Copy current registry entry to avoid mutating internal
                         # registry state before explicit restore().