### 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)
set_process(true);
		scan_total = 0;
		Thread::Settings s;
		s.priority = Thread::PRIORITY_LOW;
		thread_sources.start(_thread_func_sources, this, s);
	}
}
void EditorFileSystem::_notification(int p_what) {
	switch (p_what) {
		case NOTIFICATION_EXIT_TREE: {
			Thread &active_thread = thread.is_started() ? thread : thread_sources;
			if (use_threads && active_thread.is_started()) {
				while (scanning) {
					OS::get_singleton()->delay_usec(1000);
				}
				active_thread.wait_to_finish();
				WARN_PRINT("Scan thread aborted...");
				set_process(false);
			}
			if (filesystem) {
				memdelete(filesystem);
			}
			if (new_filesystem) {
				memdelete(new_filesystem);
			}
			filesystem = nullptr;
			new_filesystem = nullptr;
		} break;
		case NOTIFICATION_PROCESS: {
			if (use_threads) {