### 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
for (const KeyValue<String, Vector<String>> &E : group_files) {
			pr.step(E.key.get_file(), from++);
			Error err = _reimport_group(E.key, E.value);
			reloads.push_back(E.key);
			reloads.append_array(E.value);
			if (err == OK) {
				_reimport_file(E.key);
			}
		}
	}
	ResourceUID::get_singleton()->update_cache(); 
	_save_filesystem_cache();
	importing = false;
	if (!is_scanning()) {
		emit_signal(SNAME("filesystem_changed"));
	}
	emit_signal(SNAME("resources_reimported"), reloads);
}
Error EditorFileSystem::reimport_append(const String &p_file, const HashMap<StringName, Variant> &p_custom_options, const String &p_custom_importer, Variant p_generator_parameters) {
	ERR_FAIL_COND_V_MSG(!importing, ERR_INVALID_PARAMETER, "Can only append files to import during a current reimport process.");
	return _reimport_file(p_file, p_custom_options, p_custom_importer, &p_generator_parameters);
}
Error EditorFileSystem::_resource_import(const String &p_path) {
	Vector<String> files;
	files.push_back(p_path);
	singleton->update_file(p_path);
	singleton->reimport_files(files);
	return OK;
}
bool EditorFileSystem::_should_skip_directory(const String &p_path) {