Almost certainly what happened there was excess ghost sectors on SABRE. When you book across airlines like BA on Amadeus and AA or AS, both on SABRE, the main ticket is hosted on Amadeus and a ropey interface creates sectors under a new PNR in SABRE. If you change a booking or flights get cancelled or codeshares are rebuilt, there will be a set of ghost sectors that AA can see but aren't sufficient for them to rebuild, let alone get you a boarding pass. Occasionally a really clued up AA agent has Amadeus access and can rebuild things from scratch on the near empty SABRE sector, or the simple act of deleting all the SABRE PNRs and then reissuing the Amadeus ticket sorts it all out. I have heard of cases where BA has ended up redoing the reservation from scratch with a brand new PNR and then killing off the old PNR, but that is awkward in accountancy terms.

It doesn't happen often but we do see this and similar cases every few months here.