Having gone through this very issue on something like three times in the last couple of days, I think my experience is as follows:

1. It's a pain in the butt.

2. If you have a confirmed upgrade, forget about doing anything on the web.

3. For my last itinerary, a mistake had been made on the last leg YVR-YYC (off by one day; instead of a connection, we would have had to spend a bit over a day at YVR -I guess the original agent did not believe a flight from Asia would arrive on the same day-). Upgrades were confirmed on all the AC legs. When I called back a couple of hours after purchasing the ticket, to correct the mistake, the simplest way the guy found to fix this was to cancel the ticket, but keeping the reservation, to issue a new ticket. Took close to one hour, for sure more than 30 minutes, on the phone.

When you buy a refundable fare, you actually pay for their extra work. What you don't really expect is how much of a pain it can be on your side if you want to take advantage of the flexibility you paid for.