### 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
late_update_files.insert(p_file);
		_save_late_updated_files(); 
	}
	fs->files[cpos]->type = type;
	fs->files[cpos]->resource_script_class = script_class;
	fs->files[cpos]->uid = uid;
	fs->files[cpos]->script_class_name = _get_global_script_class(type, p_file, &fs->files[cpos]->script_class_extends, &fs->files[cpos]->script_class_icon_path);
	fs->files[cpos]->import_group_file = ResourceLoader::get_import_group_file(p_file);
	fs->files[cpos]->modified_time = FileAccess::get_modified_time(p_file);
	fs->files[cpos]->deps = _get_dependencies(p_file);
	fs->files[cpos]->import_valid = type == "TextFile" ? true : ResourceLoader::is_import_valid(p_file);
	if (uid != ResourceUID::INVALID_ID) {
		if (ResourceUID::get_singleton()->has_id(uid)) {
			ResourceUID::get_singleton()->set_id(uid, p_file);
		} else {
			ResourceUID::get_singleton()->add_id(uid, p_file);
		}
		ResourceUID::get_singleton()->update_cache();
	}
	
	EditorResourcePreview::get_singleton()->check_for_invalidation(p_file);
	if (ClassDB::is_parent_class(fs->files[cpos]->type, SNAME("Script"))) {
		_queue_update_script_class(p_file);
	}
	_update_pending_script_classes();
	call_deferred(SNAME("emit_signal"), "filesystem_changed"); 
}
HashSet<String> EditorFileSystem::get_valid_extensions() const {