The original booking was pretty simple, XXX-LHR-ARN-LHR-XXX roundtrip with the first and last flights on AA and the two middle flights on BA with AA codeshare flight numbers.
The AA website showed one AA PNR and one BA PNR, as expected, and I was able to choose seats for free on both BA flights on the BA website (AA OWS status), So far, so good.

Because one of the timing of the LHR-XXX return flight was changed by several hours, I was automatically rebooked on different AA flights (flying LHR-ORD-XXX on AA instead of the original LHR-XXX flight). No changes to the BA flights.

I called AA to request a better itinerary, and the reservation agent rebooked the ARN-LHR BA flight (with a BA flight number, not an AA codeshare number) so that I could make the nonstop LHR-XXX flight and avoid an extra connection.
Looking at the reservation on aa.com, it now shows a new BA PNR for the return leg.
LHR-ARN: the original BA PNR (PNR #1)
ARN-LHR: a new BA PNR (PNR #2)

Pulling up the two PNRs on ba.com shows some differing info.

BA PNR #1:
- Immediately after the rebooking, it showed all four flights in the itinerary.
- It now shows only the XXX-LHR-ARN flights, and the LHR-ARN leg is shown with the BA flight number.
- My previous seat choice was retained.

BA PNR #2:
- Shows the LHR-ARN-LHR-XXX flights.
- It didn't have my AA FF# in there, and originally showed that I had to pay for choosing a seat for the ARN-LHR flight.
- Shows the LHR-ARN flight with the AA codeshare number ("AA6529, Economy, Information only"). No chosen seat is shown for the LHR-ARN flight, and the "Choose Seat" option results in "Seat choice available at check-in." As indicated in PNR #1, I already have a seat chosen for this flight.
- After adding my AA FF#, I was able to choose a seat for free for the ARN-LHR leg.

The only slightly worrying part is the fact that PNR #2 shows the LHR-ARN flight that is under PNR #1, and the seat choice made in PNR #1 isn't reflected in PNR #2. Not sure if I should worry about that, nor do I know if I should worry about the two BA PNRs showing the same LHR-ARN flight with two different flight numbers (BA number vs. AA codeshare number).
I obviously don't want the BA system to think I no-showed on the LHR-ARN flight and therefore cancel the return ARN-LHR-XXX flights, but perhaps I don't need to worry about that?