I recently have an experience with this. Flew TPE-NRT-YVR, 1st leg on UA, 2nd on AC. I wanted to check 2 bags, so I must have AC status on file.

Called UA 3 times, first two times the agents have no idea about "2 fields" (BTW, the calls seem to connect to India). The third agent stated that she used to be able to put 2 FFP numbers, but after CO/UA merger, the system does not have the capability. (was on the phone for 30 mins, she asked her support team numerous times) To no avail, she offered to put a note on my PNR. At check-in, the agent refused to check 2 bags with UA MP#. It was just a 3 hr flight so did not bother to argue.

My upgrade for NRT-YVR cleared a day before, so I checked in online and changed the number to UA MP. Since the BP was in J, so I had no problem entering lounges. I assume it would've been a hassle as well if I was to travel in Y.

Can anyone provide some insights to this? (Having 2 #s on PNR)