Odd situation here — dealing with a BOS-JFK-HND-ITM itinerary about two weeks out. First leg is on B6; rest is on JL. I initially held the JFK-HND, and had an agent add the BOS-JFK and HND-ITM segments earlier today.

Went just now to ticket it, and the B6 BOS-JFK segment had disappeared. Called AA; agent was puzzled, but managed to re-add the segment, assign seats on B6, and process payment for the flight.

I just went back to the PNR — which is currently "on request" — and the BOS-JFK B6 segment has once again disappeared.

I have screenshots of the PNR from both times when the B6 segment was in the record, including the B6 PNRs. Is it reasonable to assume AA will find some way to fix this, either by reinstating the B6 flight or opening space on the similarly timed YX flight?