I had a LAX-LHR booking, upgraded using miles, on which I tried the website repricing option. Man, what an ordeal this turned out to be....

The repricing tool offered me a refund of $42.00. I said "Great", but decided to call the 1K line ( Mother created no fool) to make sure that if I went ahead, nothing would happen to my upgrades.

So while I have the page still up, I get a res agent and ask whether I am in any danger of losing the upgrades at all. "No", she said, the only thing you are doing is repricing the itinerary.

And of course guess what, as soon as I hit "Finalize" my new itinerary comes up, my upgrades are gone. Why? Because the new itinerary was booked in Q vs H (hence the $42.00 difference).

She and a supervisor could not get my upgrades back and they asked me to call web support, who had no clue why I had been sent there since they have no ability to make a reservation.

I ended up having to return to the 1K desk, and my entire itinerary was cancelled, rebooked (now for a fare higher by $22 ) and I was lucky enough to get my upgrades back.

Lesson: Beware on upgraded reservations. This system should let you know if it is rebooking you on a non-upgradeable fare instead of keeping you in the same fare class...