I had a somewhat similar event happened last week - upgrade cleared IAD/GRU after configuration change to new config. GA says there are no FC seats available so board with my original seat. Upgrade gone from my account, but not shown as used - don't know where it went. Wrote GS customer service and they gave me 10,000 miles and apologized for the plane change - but no explanation as to how upgrade cleared after the plane change if there were no seats and no explanation of where the upgrade went - probably doesn't matter since it was due to expire today. I guess I should feel fortunate that they did not upgrade someone into my old C-class seat.
UAL GS is not what it used to be.