### 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)
}
		if (da->current_is_dir()) {
			if (f.begins_with(".")) { 
				continue;
			}
			if (_should_skip_directory(cd.path_join(f))) {
				continue;
			}
			dirs.push_back(f);
		} else {
			files.push_back(f);
		}
	}
	da->list_dir_end();
	dirs.sort_custom<NaturalNoCaseComparator>();
	files.sort_custom<NaturalNoCaseComparator>();
	int total = dirs.size() + files.size();
	int idx = 0;
	for (List<String>::Element *E = dirs.front(); E; E = E->next(), idx++) {
		if (da->change_dir(E->get()) == OK) {
			String d = da->get_current_dir();
			if (d == cd || !d.begins_with(cd)) {
				da->change_dir(cd); 
			} else {
				EditorFileSystemDirectory *efd = memnew(EditorFileSystemDirectory);
				efd->parent = p_dir;
				efd->name = E->get();
				_scan_new_dir(efd, da, p_progress.get_sub(idx, total));
				int idx2 = 0;
				for (int i = 0; i < p_dir->subdirs.size(); i++) {