### 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)
scan_actions.push_back(ia);
			continue;
		}
		_scan_fs_changes(p_dir->get_subdir(i), p_progress);
	}
}
void EditorFileSystem::_delete_internal_files(String p_file) {
	if (FileAccess::exists(p_file + ".import")) {
		List<String> paths;
		ResourceFormatImporter::get_singleton()->get_internal_resource_path_list(p_file, &paths);
		Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		for (const String &E : paths) {
			da->remove(E);
		}
		da->remove(p_file + ".import");
	}
}
void EditorFileSystem::_thread_func_sources(void *_userdata) {
	EditorFileSystem *efs = (EditorFileSystem *)_userdata;
	if (efs->filesystem) {
		EditorProgressBG pr("sources", TTR("ScanSources"), 1000);
		ScanProgress sp;
		sp.progress = &pr;
		sp.hi = 1;
		sp.low = 0;
		efs->_scan_fs_changes(efs->filesystem, sp);
	}
	efs->scanning_changes_done = true;
}
void EditorFileSystem::scan_changes() {