The miles should come back to your AA account -- whichever was withdrawn from. Are you putting her frequent flier just for the Secure Traveler info? You should be able to get the miles back as long as you cancel the before the flight departs (phone or online). I would do it as early as you can just to be safe but theoretically you can do it a few minutes before.
https://www.aa.com/i18n/aadvantage-p...ard-travel.jsp
Canceling upgrade awards and reinstating miles
If your plans change and you no longer wish to travel or upgrade your ticket, you can contact Reservations to cancel your mileage upgrade award and request reinstatement of your miles. If you cancel your trip on aa.com, you must contact Reservations to request the reinstatement of your miles.
We’ll reinstate your miles at no charge up to 1 year after the ticket issue date, but you have to cancel your ticket before the first flight departs.
Contact Reservations
Refunds of taxes and fees will be issued in full amounts, less:
- Sale-imposed nonrefundable taxes
- Taxes we must pay whether or not you travel
Keep in mind, co-payments for mileage upgrade awards are non-refundable and tickets upgraded with mileage upgrade awards retain all the original fare rules and restrictions of the original purchased fare.