I had similar situation, though my outbound wasn't sold out. I needed to change my return flight. (of a 4 seg itin). I had rec'd upgrades on the first 3 segs, but not the last one which I needed to change. They couldn't just change the one. The corp travel suggested I wait until I fly all 3 legs and then call to secure the upgrades, but didn't want this option as the return flight price could go way up. I looked into using miles for the return portion, and cancelling the last leg, but was told that's a no-go too, as they would re-price the entire thing, and it would likely go way up.
I therefore just reticketed the entire thing, lost my 3 upgrades, and paid the fare diff, and change fees. I had been told US could "add back" my upgrades after the ticket was issued. This was not true. They said they can only do that manually at 24hr window. so now I'm left hoping at the sweep tonight, they all get reprocessed.
As this was entirely my fault, I am not blaming US, even though it would have been nice,if I could have just changed the return flight and kept the other 3 intact. I realize there are laws/regs/procedures preventing this. Just an observation that it would have been nice.
Also, any thoughts on whether my 3 UGs will clear? I guess they should unless, someone of higher miles and CP happens to book these segs.
Cheers