Thank you I will give BA a try tomorrow. I was able to do seat selection for one of the flights with BA over the phone a few days ago (and that did propagate through to the AA website where I can see those seats are now selected), I just didn't do all of my BA sectors.

I guess the ultimate question is: this is an AA booking, it was an AA flight (AA metal) that was changed, and AA says the ticket was issued - is it actually likely there's any chance of an issue when we go to check in? Would definitely like to get it fixed though.