### 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)
}
		Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
		d->remove(update_cache); 
	}
	EditorProgressBG scan_progress("efs", "ScanFS", 1000);
	ScanProgress sp;
	sp.low = 0;
	sp.hi = 1;
	sp.progress = &scan_progress;
	new_filesystem = memnew(EditorFileSystemDirectory);
	new_filesystem->parent = nullptr;
	Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_RESOURCES);
	d->change_dir("res://");
	_scan_new_dir(new_filesystem, d, sp);
	file_cache.clear(); 
	if (!first_scan) {
		
		_save_filesystem_cache();
	}
	scanning = false;
}
void EditorFileSystem::_save_filesystem_cache() {
	group_file_cache.clear();
	String fscache = EditorPaths::get_singleton()->get_project_settings_dir().path_join(CACHE_FILE_NAME);
	Ref<FileAccess> f = FileAccess::open(fscache, FileAccess::WRITE);
	ERR_FAIL_COND_MSG(f.is_null(), "Cannot create file '" + fscache + "'. Check user write permissions.");
	f->store_line(filesystem_settings_version_for_import);
	_save_filesystem_cache(filesystem, f);
}
void EditorFileSystem::_thread_func(void *_userdata) {