### 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
config->get_section_keys("params", &sk);
			for (const String &param : sk) {
				Variant value = config->get_value("params", param);
				
				source_file_options[p_files[i]][param] = value;
			}
		}
		base_paths[p_files[i]] = ResourceFormatImporter::get_singleton()->get_import_base_path(p_files[i]);
	}
	if (importer_name == "keep") {
		return OK; 
	}
	ERR_FAIL_COND_V(importer_name.is_empty(), ERR_UNCONFIGURED);
	Ref<ResourceImporter> importer = ResourceFormatImporter::get_singleton()->get_importer_by_name(importer_name);
	Error err = importer->import_group_file(p_group_file, source_file_options, base_paths);
	
	for (const KeyValue<String, HashMap<StringName, Variant>> &E : source_file_options) {
		const String &file = E.key;
		String base_path = ResourceFormatImporter::get_singleton()->get_import_base_path(file);
		Vector<String> dest_paths;
		ResourceUID::ID uid = uids[file];
		{
			Ref<FileAccess> f = FileAccess::open(file + ".import", FileAccess::WRITE);
			ERR_FAIL_COND_V_MSG(f.is_null(), ERR_FILE_CANT_OPEN, "Cannot open import file '" + file + ".import'.");
			
			f->store_line("[remap]");
			f->store_line("");
			f->store_line("importer=\"" + importer->get_importer_name() + "\"");
			int version = importer->get_format_version();
			if (version > 0) {