Don't waste anymore time on the phone. For whatever reason, these codeshare flights are a huge mess when any upgrade clears. I've learned the hard way that trying to resolve it over the phone seems to make it worse, not better. I now wait until the airport for check in. I don't buy the CO rep claiming the issue is on UA's end, I'm convinced its CO's system that is causing the headache.
Twice now a fellow FT'r and I have experimented with this. Identical bookings for both of us, booked via CO with UA metal. I try to check in online and he waits until the airport. I get an error, try to talk to reps, then get to the aiport, spend more time with the agent working with it, but my friend seems to have no problem if he waits until the airport for check in. Airport agent claimed I made it worse by trying to check in online, so I no longer do this...