### Godot version

v4.1.beta.custom_build [72b59325c]

### System information

Windows 10, Vulkan

### Issue description

This has been plaguing me for a while in my main project. I can only partially reproduce it in a MRP:
When placing a binary mesh resource imported from a .glb file into a MeshInstance3D, it will be gone upon restart. It doesn't seem to happen to every resource, but I've had MIs that were fine and then start doing it out of nowhere.
I thought it was going to be related to materials due to things like https://github.com/godotengine/godot/issues/77007 but I can reliably trigger it with the steps listed below.
I have done limited testing on .tres files because I usually use .res for size/performance, but in the MRP .tres doesn't seem to trigger it, so perhaps it doesn't affect those.

Note on the Steps to reproduce: you have to delete the test_cube.res and redo the steps to trigger the bug again, but in my main project the affected resources always disappear.

### Steps to reproduce

1. Double click test_cube.glb
2. Click the mesh (test_cube_Cube_097), set save to file path as: res://test_cube.res
3. Make sure to click the little folder icon and then Save (this seems to make it consistent to proc)
4. Press Reimport
5. Drag the test_cube.res to the Mesh slot of the MeshInstance3D
6. Ctrl+s to save
7. Project -> Reload current project
8. Mesh is no longer in the MeshInstance3D

### Minimal reproduction project

[binary res bug.zip](https://github.com/godotengine/godot/files/11681009/binary.res.bug.zip)
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) {