### 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)
memdelete(filesystem);
					}
					filesystem = new_filesystem;
					new_filesystem = nullptr;
					thread.wait_to_finish();
					_update_scan_actions();
					_update_pending_script_classes();
					emit_signal(SNAME("filesystem_changed"));
					emit_signal(SNAME("sources_changed"), sources_changed.size() > 0);
					first_scan = false;
				}
				if (done_importing && scan_changes_pending) {
					scan_changes_pending = false;
					scan_changes();
				}
				prevent_recursive_process_hack = false;
			}
		} break;
	}
}
bool EditorFileSystem::is_scanning() const {
	return scanning || scanning_changes;
}
float EditorFileSystem::get_scanning_progress() const {
	return scan_total;
}
EditorFileSystemDirectory *EditorFileSystem::get_filesystem() {
	return filesystem;
}
void EditorFileSystem::_save_filesystem_cache(EditorFileSystemDirectory *p_dir, Ref<FileAccess> p_file) {