I had an interesting experience with getting miles for upgrades. I decided to use my ROP Gold renewal certificate against a AKL-SYD-BKK paid ticket. TG in Auckland reissued the ticket as J Class. When it came to the points, they originally gave me J Class points, then a couple of months later someone must have done an audit, as they adjusted the points down to Economy Class. However on the return leg they're still sitting there as J Class. As I'm also a UA 1K member, I'm wondering if I make my booking, get my upgrdae certificate applied, get a re-issued ticket and then change the FF# from ROP to Mileage Plus - would I get J or Y points?

But to return to the point - once the upgrade certificate has been applied you can readily change those flights also, as they simply appear as a J Class booking