### 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
f->store_line("[params]");
			f->store_line("");
			
			List<ResourceImporter::ImportOption> options;
			importer->get_import_options(file, &options);
			
			for (const ResourceImporter::ImportOption &F : options) {
				String base = F.option.name;
				Variant v = F.default_value;
				if (source_file_options[file].has(base)) {
					v = source_file_options[file][base];
				}
				String value;
				VariantWriter::write_to_string(v, value);
				f->store_line(base + "=" + value);
			}
		}
		
		{
			Ref<FileAccess> md5s = FileAccess::open(base_path + ".md5", FileAccess::WRITE);
			ERR_FAIL_COND_V_MSG(md5s.is_null(), ERR_FILE_CANT_OPEN, "Cannot open MD5 file '" + base_path + ".md5'.");
			md5s->store_line("source_md5=\"" + FileAccess::get_md5(file) + "\"");
			if (dest_paths.size()) {
				md5s->store_line("dest_md5=\"" + FileAccess::get_multiple_md5(dest_paths) + "\"\n");
			}
		}
		EditorFileSystemDirectory *fs = nullptr;
		int cpos = -1;
		bool found = _find_file(file, &fs, cpos);
		ERR_FAIL_COND_V_MSG(!found, ERR_UNCONFIGURED, "Can't find file '" + file + "'.");