### 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)
if (dest_paths.size()) {
			md5s->store_line("dest_md5=\"" + FileAccess::get_multiple_md5(dest_paths) + "\"\n");
		}
	}
	
	fs->files[cpos]->modified_time = FileAccess::get_modified_time(p_file);
	fs->files[cpos]->import_modified_time = FileAccess::get_modified_time(p_file + ".import");
	fs->files[cpos]->deps = _get_dependencies(p_file);
	fs->files[cpos]->type = importer->get_resource_type();
	fs->files[cpos]->uid = uid;
	fs->files[cpos]->import_valid = fs->files[cpos]->type == "TextFile" ? true : ResourceLoader::is_import_valid(p_file);
	if (ResourceUID::get_singleton()->has_id(uid)) {
		ResourceUID::get_singleton()->set_id(uid, p_file);
	} else {
		ResourceUID::get_singleton()->add_id(uid, p_file);
	}
	
	
	Ref<Resource> r = ResourceCache::get_ref(p_file);
	if (r.is_valid()) {
		if (!r->get_import_path().is_empty()) {
			String dst_path = ResourceFormatImporter::get_singleton()->get_internal_resource_path(p_file);
			r->set_import_path(dst_path);
			r->set_import_last_modified_time(0);
		}
	}
	EditorResourcePreview::get_singleton()->check_for_invalidation(p_file);
	return OK;
}
void EditorFileSystem::_find_group_files(EditorFileSystemDirectory *efd, HashMap<String, Vector<String>> &group_files, HashSet<String> &groups_to_reimport) {