### 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)
continue;
		}
		if (use_multiple_threads && reimport_files[i].threaded) {
			if (i + 1 == reimport_files.size() || reimport_files[i + 1].importer != reimport_files[from].importer) {
				if (from - i == 0) {
					
					pr.step(reimport_files[i].path.get_file(), i);
					_reimport_file(reimport_files[i].path);
				} else {
					Ref<ResourceImporter> importer = ResourceFormatImporter::get_singleton()->get_importer_by_name(reimport_files[from].importer);
					ERR_CONTINUE(!importer.is_valid());
					importer->import_threaded_begin();
					ImportThreadData tdata;
					tdata.max_index = from;
					tdata.reimport_from = from;
					tdata.reimport_files = reimport_files.ptr();
					WorkerThreadPool::GroupID group_task = WorkerThreadPool::get_singleton()->add_template_group_task(this, &EditorFileSystem::_reimport_thread, &tdata, i - from + 1, -1, false, vformat(TTR("Import resources of type: %s"), reimport_files[from].importer));
					int current_index = from - 1;
					do {
						if (current_index < tdata.max_index) {
							current_index = tdata.max_index;
							pr.step(reimport_files[current_index].path.get_file(), current_index);
						}
						OS::get_singleton()->delay_usec(1);
					} while (!WorkerThreadPool::get_singleton()->is_group_task_completed(group_task));
					WorkerThreadPool::get_singleton()->wait_for_group_task_completion(group_task);
					importer->import_threaded_end();
				}
				from = i + 1;
			}