### 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)
update_script_mutex.lock();
	for (const String &path : update_script_paths) {
		ScriptServer::remove_global_class_by_path(path); 
		int index = -1;
		EditorFileSystemDirectory *efd = find_file(path, &index);
		if (!efd || index < 0) {
			
			continue;
		}
		if (!efd->files[index]->script_class_name.is_empty()) {
			String lang;
			for (int j = 0; j < ScriptServer::get_language_count(); j++) {
				if (ScriptServer::get_language(j)->handles_global_class_type(efd->files[index]->type)) {
					lang = ScriptServer::get_language(j)->get_name();
				}
			}
			if (lang.is_empty()) {
				continue; 
			}
			ScriptServer::add_global_class(efd->files[index]->script_class_name, efd->files[index]->script_class_extends, lang, path);
			EditorNode::get_editor_data().script_class_set_icon_path(efd->files[index]->script_class_name, efd->files[index]->script_class_icon_path);
			EditorNode::get_editor_data().script_class_set_name(path, efd->files[index]->script_class_name);
		}
	}
	
	for (const String &path : update_script_paths) {
		int index = -1;
		EditorFileSystemDirectory *efd = find_file(path, &index);
		if (!efd || index < 0) {