I am having a similar problem at the moment.
Bought a ticket from aa online from UK for DUB-LHR-PHL-PHX-KOA-LAX-PHX-BOS-LHR-DUB. The US domestic segments all on AA metal with AA codes. Everything apart from PHL-PHX booked into P and has posted correctly. I did have a re-routing as a result of a schedule change which I got changed back to the original route as above and the PHL-PHX segment was affected by that. However, the original ticket and the revised ticket both show it as booked into A.
The PHL-PHX segment which was booked into A has posted as Y. I queried this a couple of weeks ago via the webform as a general query (following advice I found on here but now can't find again). I got a reply today saying
"American Airlines have confirmed your flight has already been correctly credited, which you can see if you log in to your account at ba.com.
I hope this is helpful and I do hope you fly with us again soon."
Well obviously that wasn't helpful! I used the link in that email to reply and say, nicely, that I didn't think that was right. Last time I queried a reply, albeit on a different issue, by that route it got picked up by the GGL team and I got a sensible reply a day or so later.
I appreciate this isn't helping the OP - just showing some solidarity. My plan is to see what happens in response to my latest message in the hope that it will be resolved. If not I'll try
BAMissingAvios.
Fingers crossed - for me and OP.