### 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)
_reimport_file(p_file, p_custom_params, p_importer);
	
	Vector<String> reloads;
	reloads.append(p_file);
	emit_signal(SNAME("resources_reimported"), reloads);
}
void EditorFileSystem::_reimport_thread(uint32_t p_index, ImportThreadData *p_import_data) {
	p_import_data->max_index = MAX(p_import_data->reimport_from + int(p_index), p_import_data->max_index);
	_reimport_file(p_import_data->reimport_files[p_import_data->reimport_from + p_index].path);
}
void EditorFileSystem::reimport_files(const Vector<String> &p_files) {
	ERR_FAIL_COND_MSG(importing, "Attempted to call reimport_files() recursively, this is not allowed.");
	importing = true;
	Vector<String> reloads;
	EditorProgress pr("reimport", TTR("(Re)Importing Assets"), p_files.size());
	Vector<ImportFile> reimport_files;
	HashSet<String> groups_to_reimport;
	for (int i = 0; i < p_files.size(); i++) {
		String file = p_files[i];
		ResourceUID::ID uid = ResourceUID::get_singleton()->text_to_id(file);
		if (uid != ResourceUID::INVALID_ID && ResourceUID::get_singleton()->has_id(uid)) {
			file = ResourceUID::get_singleton()->get_id_path(uid);
		}
		String group_file = ResourceFormatImporter::get_singleton()->get_import_group_file(file);
		if (group_file_cache.has(file)) {