Was the primary cardholder also one of the passengers ticketed for the flight itinerary?

Whom are they speaking with on the phone for 3 hours that can't get a manager or floor supervisor on the phone to find an answer?

Generally anytime I book an itinerary through amex travel, be it hotel or flight (using MR), they will immediately debit the cash value from the card, then proceed to process the points equivalent and give statement credits within 24-48 hours. So that is typically a paper trail I look for, and confirmation numbers are furnished in email virtually immediately.

If the cardholder has email proof of the confirmation number (print out/digital), or a valid confirmation number inside AMEX's system, It would be pretty difficult for them not to accept responsibility, unless I am missing something.

Entire thing sounds like a massive nightmare, wish them luck.