Similar question, yesterday I bought a day of departure upgrade on the second leg of my trip.
Due to MX delay (our Dreamliner had a dead battery), I nearly missed my connection.
As a matter of fact, I walked off my inbound, outbound gate was 20 steps away so I gave it a shot.
They had to check me back in, and of course my seat was already gone.
Tricky part is, no boarding pass or anything showing the buy-up, but I did get PQPs for it...
Should I just wait to see if the charge gets backed out?