Since AA appears to be waiting until the very last minute to clear SWU upgrades this is going to be a more frequent problem. Traditionally, the SWU for the international portion would clear early enough that there was still plenty of A inventory for the domestic portion. But if they are waiting until D-1 or D-2 to clear the international portion, then all other EXPs and even Plats will have cleared on the domestic flight before you even get a shot.
A couple of weeks before a trip to Europe last month, I went ahead and had them pull the SWUs, clear the domestic legs, and stay waitlisted for the rest. It was a good thing I did. By the time the TATL flights cleared (D-2 in both directions) the F cabin between AUS and JFK was almost full.