So, it would seem that the underlying fare basis can hang around in the record in some cases.
Yeah, I tried something similar this year when I was rebooked the day of a flight due to a delay. I ended up on a JFK-GRU flight in Y when my original ticket was in Q. I asked three agents to upgrade me, and all three said it was no problem and that no co-pay was required. Then after a minute or two came the "Oh, wait..." and denial.