### Godot version

v4.0.beta.custom_build [0a9e6e478]

### System information

Windows 10, Vulkan, GTX 960 528.24

### Issue description

This [55420](https://github.com/godotengine/godot/issues/55420) issue seems that it is not completely solved since in the advanced importer the same thing continues to happen.

### Steps to reproduce

- Put a 3D model on the scene
- Open the advanced import
- Disable Auto LOD or whatever you want to change
- See how mesh doesn't change

### Minimal reproduction project

N/A
String project_data_path = ProjectSettings::get_singleton()->get_project_data_path();
	if (p_path == project_data_path || p_path.begins_with(project_data_path + "/")) {
		return true;
	}
	if (FileAccess::exists(p_path.path_join("project.godot"))) {
		
		return true;
	}
	if (FileAccess::exists(p_path.path_join(".gdignore"))) {
		
		return true;
	}
	return false;
}
bool EditorFileSystem::is_group_file(const String &p_path) const {
	return group_file_cache.has(p_path);
}
void EditorFileSystem::_move_group_files(EditorFileSystemDirectory *efd, const String &p_group_file, const String &p_new_location) {
	int fc = efd->files.size();
	EditorFileSystemDirectory::FileInfo *const *files = efd->files.ptrw();
	for (int i = 0; i < fc; i++) {
		if (files[i]->import_group_file == p_group_file) {
			files[i]->import_group_file = p_new_location;
			Ref<ConfigFile> config;
			config.instantiate();
			String path = efd->get_file_path(i) + ".import";
			Error err = config->load(path);
			if (err != OK) {
				continue;