I've actually dealt with this issue multiple times. Don't take it for granted that the check-in agent will allow you the online baggage allowance as the issuing airline needs to put that information on the ticket. So what I ended up doing is asking an AA rep to put a note in the reservation for the baggage allowance whereby the check-in agent would be able see it at the airport. Then I'd call Etihad to confirm that they see it too. If no notes are there, they have every right to charge you for the bags as it needs to be clearly indicated on the ticket and they don't assume anything in these instances.