### 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 (!first_scan) {
				EditorNode::get_singleton()->save_all_scenes();
			}
			EditorNode::get_singleton()->restart_editor();
			
			return true;
		}
	}
	if (reimports.size()) {
		if (_scan_import_support(reimports)) {
			return true;
		}
		reimport_files(reimports);
	} else {
		
		ResourceUID::get_singleton()->update_cache();
	}
	if (first_scan) {
		
		revalidate_import_files = false;
		filesystem_settings_version_for_import = ResourceFormatImporter::get_singleton()->get_import_settings_hash();
		_save_filesystem_cache();
	}
	if (reloads.size()) {
		emit_signal(SNAME("resources_reload"), reloads);
	}
	scan_actions.clear();
	return fs_changed;
}
void EditorFileSystem::scan() {