Technically the rule is that you do forfeit the fees that you have paid. On several occasions though I have simply called and did the upgrade over the phone and mentioned the fee and the Agent refunded the Preferred/Comfort+ seat without any problem. So YMMV, but I think if you call and just ask nicely when they are processing the upgrade you have a decent shot at getting it refunded. I had this happen most recently 3 or so days ago.