Booked 2 separate PNRs GVA-LHR-IAD-BOS, with GVA-LHR on LX, with a 14hr overnight stop in LHR, but ticketed in coach with no APD (of course).
Applied a GPU online for one PNR and was charged $100 add-collect for the fictitious APD which I am pretty sure is not actually owed.
Applied a GPU by phone to the other PNR and the phone agent said something a little unclear (I didn't hear him very well) about having to pay an extra departure tax when I check in at the airport, but I said, hm, I think that's unlikely since I'm traveling GVA-BOS and just in transit at LHR, and he said, fair enough, guess you'll see at the airport!.
The eticket on the 'bad' pnr says
Additional Charges: Thu., Mar. 3, 2016/Visa .... was charged 100 USD for the SST / EDD 016..........
100.00 USD for: APD Tax Difference /For UK Use Only/
Now let's see whether the $100 that was incorrectly charged on the first PNR will ever,ever,ever,ever come back. I guess I can file a refund request.
Edit: actually, what I did was call a UA phone agent and say, hi, just calling to check that the upgrade was confirmed? Great, now can you confirm whether an APD was charged? (Yes, it was.) Should it have been? She's only in transit, but I know the UA web site has a bug sometimes. (Oh, she says. Let me check if we charged the $100, if so we'll refund it.)
I'm still on hold but this seems pretty painless!
Edit: OK, refunded! Great agent.