Hi Isobel,
The top level menu item for the quick links is hardcoded to have the internal ID of 3 in the database.
If you want to create a new root menu item with that ID the easiest way to do it is with a schort PHP script that you can download into the root director of AtoM then run. You should delete the quick links you recreated before downloading and running this script.
Here's how to download and run the script:
$ cd /path/to/atom
$ php symfony tools:run fix.php
After running this script you should end up with a new top level menu item for quick links that you can manually re-add items to.
Let me know if you have any questions!
Cheers,
Mike Cantelon
Artefactual Systems