If your purchase was the second of two $100 *cough* seat upgrades *cough*, then I don't think you have anything to worry about. Worst case, if AA does not reimburse for whatever reason, you have moved $100 from one pocket to another. The reimbursement can be pocketed another day.
The weird world, as I tried to explain earlier, is for those of us for whom this was the first $100 card usage. Ironically (paradoxically?), the problem comes if this double charge triggers two reimbursements. Yes, we can get one of them taken off, eventually, but we won't have anything to show for that second $100, and will have to trust the Amex system to credit us yet again on a later $100 charge.
The paradox here is that I am dreading seeing, tomorrow, two reimbursements. Better none!