Originally Posted by corporate-wage-slave

The process for AUPs is convoluted and that's noticeable at LHR when there is a call to Flight Control to release the seat - the agent can see the AUP price and the computer appears OK to release the seat, but there is manual process to finalise the AUP for the various factors which are not on the computer - irrops, space available upgrades for previous flights. Older readers will recall there was an arbitrary limit to how many AUPs you could have at one point, but that appears to have faded away. At out-stations the station manager would normally tell check-in staff before check-in opens "we need to upsell 4 in J and 1 in F today" or some such and that's easy enough to control that at IAD and anywhere other than JFK. Here some miscommunication happened, a one off screw up, and the OP was the fall guy.

BA will want to get away with a refund of the AUP, but EC261 clearly would apply here for the reimbursement (not compensation) and under Mennens (see wiki of main EC261 thread) the baseline is 75% of the fare paid, pro-rata for the distance, and with BA able to collect any necessary taxes and airport fees. Probably around 60% of the original fare (after halving for distance) plus the AUP in full. Even if BA were agreeable to this it would take weeks to calculate. There is a high chance it will go to CEDR so the OP should do the maths, as per the wiki, so as to ensure they are not short-changed. Hopefully they didn't buy the ticket from AA......