Even if the AA website would allow updating the passport information at online check-in time, this cannot be assumed to occur before any APIS data transmission to the destination country's border authorities, so that might still be later than desired for the purposes of my original concern.

About ETA/ESTA/ETIAS, this might prevent checking in online, but you can provide the correct passport for *this* leg at airport check-in, and unless the just-in-time system finds something really suspicious about it you'll still be able to travel that day, just maybe with extra personal attention at the security checkpoint.

My concern is that not all countries really love the idea of people having two nationalities, and I'd prefer ot have my US passport *not* sent ahead to my European country of nationality under any circumstances, just to avoid the highly unlikely but quite impactful possibility of uncomfortable questions being raised.