### 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
ia.dir = p_dir;
				ia.file = p_dir->files[i]->file;
				scan_actions.push_back(ia);
			}
		}
	}
	for (int i = 0; i < p_dir->subdirs.size(); i++) {
		if ((updated_dir && !p_dir->subdirs[i]->verified) || _should_skip_directory(p_dir->subdirs[i]->get_path())) {
			
			ItemAction ia;
			ia.action = ItemAction::ACTION_DIR_REMOVE;
			ia.dir = p_dir->subdirs[i];
			scan_actions.push_back(ia);
			continue;
		}
		_scan_fs_changes(p_dir->get_subdir(i), p_progress);
	}
}
void EditorFileSystem::_delete_internal_files(String p_file) {
	if (FileAccess::exists(p_file + ".import")) {
		List<String> paths;
		ResourceFormatImporter::get_singleton()->get_internal_resource_path_list(p_file, &paths);
		Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		for (const String &E : paths) {
			da->remove(E);
		}
		da->remove(p_file + ".import");
	}
}
void EditorFileSystem::_thread_func_sources(void *_userdata) {