### 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)
return false;
	}
	String f = ProjectSettings::get_singleton()->localize_path(p_file);
	if (!f.begins_with("res://")) {
		return false;
	}
	f = f.substr(6, f.length());
	f = f.replace("\\", "/");
	Vector<String> path = f.split("/");
	if (path.size() == 0) {
		return false;
	}
	String file = path[path.size() - 1];
	path.resize(path.size() - 1);
	EditorFileSystemDirectory *fs = filesystem;
	for (int i = 0; i < path.size(); i++) {
		if (path[i].begins_with(".")) {
			return false;
		}
		int idx = -1;
		for (int j = 0; j < fs->get_subdir_count(); j++) {
			if (fs->get_subdir(j)->get_name() == path[i]) {
				idx = j;
				break;
			}
		}
		if (idx == -1) {
			
			EditorFileSystemDirectory *efsd = memnew(EditorFileSystemDirectory);
			efsd->name = path[i];