It's always a bad idea to "change" something about a payment like this.

You should ring AF again and explain that you changed the payment method....I could be wrong, but from the way you described the situation, it appears that you may not have given this info on the phone during your first call. You should have a reference number (most likely the PNR) for the transaction.

However, given that the payment wasn't successfully completed, I think all that they will tell you now is to wait for the systems to realise a payment was received for which no valid booking can be reconciled - and wait for the system to process a refund.

When a bank transfer goes wrong in this manner, it usually is spotted and returned within 48 hours. However, given that you used a credit card, it can probably take much longer (weeks, perhaps) to be refunded.

I would advise you to ring AF again and give them the specific details that you added to your post here. However, I expect that there is nothing they can do, given that the original booking is now expired. You will almost certainly have to make a new booking, and the price you originally had may no longer be available. I do not think there is now any way for them to associate the stray, random payment with the now expired booking - and there may be no way for them to expedite the refund of that payment to your card.

Please keep us advised of your progress.