### 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 (import_support_queries[i]->is_active()) {
			Vector<String> extensions = import_support_queries[i]->get_file_extensions();
			for (int j = 0; j < extensions.size(); j++) {
				import_support_test.insert(extensions[j], i);
			}
		}
	}
	if (import_support_test.size() == 0) {
		return false; 
	}
	for (int i = 0; i < reimports.size(); i++) {
		HashMap<String, int>::Iterator E = import_support_test.find(reimports[i].get_extension().to_lower());
		if (E) {
			import_support_tested.write[E->value] = true;
		}
	}
	for (int i = 0; i < import_support_tested.size(); i++) {
		if (import_support_tested[i]) {
			if (import_support_queries.write[i]->query()) {
				return true;
			}
		}
	}
	return false;
}
bool EditorFileSystem::_update_scan_actions() {
	sources_changed.clear();
	bool fs_changed = false;
	Vector<String> reimports;
	Vector<String> reloads;