### 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)
int fc = efd->files.size();
	const EditorFileSystemDirectory::FileInfo *const *files = efd->files.ptr();
	for (int i = 0; i < fc; i++) {
		if (groups_to_reimport.has(files[i]->import_group_file)) {
			if (!group_files.has(files[i]->import_group_file)) {
				group_files[files[i]->import_group_file] = Vector<String>();
			}
			group_files[files[i]->import_group_file].push_back(efd->get_file_path(i));
		}
	}
	for (int i = 0; i < efd->get_subdir_count(); i++) {
		_find_group_files(efd->get_subdir(i), group_files, groups_to_reimport);
	}
}
void EditorFileSystem::reimport_file_with_custom_parameters(const String &p_file, const String &p_importer, const HashMap<StringName, Variant> &p_custom_params) {