So, it does now seem one can make online changes to itins on which flights have been upgraded. I have a YYZ-BCN LHR-YYZ ticket with YYZ-BCN in PR and LHR-YYZ in B upgraded. Previously the "change flights" button was grayed after an UG. Now I am able to price up what I may want to do, change the YYZ-BCN segment to mainline J. I am getting all the options and prices. I haven't checked if it would go all the way through to a booking, but I ilke this enhancement