I know from a friend that works at AA that when a seat is changed by the airport agent in the check-in system, that seat change is never reflected in the PNR. So any agent you talk to on the phone will still see the old seat. But the seat in the check-in system is the one that you have, and any BP issued at the airport will reflect that seat.

The real question here, I think, is why your seat was changed...but that's a different conversation.