I was flying ALB->ORD->SFO with seats booked in E+ and my reservation made with my MileagePlus account # (to get free checked bag and E+ seats since I am UA Gold). At the gate in ALB, I had the gate agent change the FF program on the reservation to ANA, since I am trying to accumulate miles there this year (I have no status on ANA). She had trouble making the change and said she had to "check me out and check me in again" (she might have said "uncheck you in"), and printed a new boarding pass for the ALB->ORD flight (I don't know if a new boarding pass for the second leg was printed).

As we lined up for boarding, I noticed the new (paper) boarding pass was now in Group 3 instead of Group 1, so I used the original boarding pass I had gotten when I checked my bag, and there was no issue. However, when I connected in ORD, there was some error when I scanned my original (paper) boarding pass for ORD->SFO, so I was taken aside and an agent was trying to figure out what the problem was. We figured it must have been related to the change in FF program and the fact that I don't have status on ANA, and she noticed that I was now in a standard E seat, and my original (window) E+ seat was no longer available! She switched me to a middle E+ seats, so the amount of inconvenience was minimal, but the experience was disturbing and I wouldn't like to go through it if my originally booked class had been filled up!

I haven't seen anything similar in other threads about changing FF programs post-checkin, so I wonder if anyone knows:

Is this kind of seat change/rebooking when changing FF programs at the airport common?

Was this the ALB gate agent's mistake, by checking me out and then checking me in again? I.e. is there a procedure she should have known about? She tried a few things before opting for the checkout, but maybe she didn't know about some other procedure.

When was my seat on the second leg reassigned? Immediately upon changing the FF info? While I was in the air? When boarding began at ORD? I.e. when is the best time to correct the reassignment?

Anyway, if you ever change your FF program info at the airport, make sure you have printed out boarding passes first, so you can prove what seats you had in case United takes them away!