I've had the same experience... I called in for a Low Fare Gaurantee refund (after being notified by TripIt Pro) and the phone agent warned that my upgrade would not return to U and, therefore, I would lose my upgrade. Since the flight was for work and had already been expensed (trying to figure out where the refund went on the company card would be problematic) and was only for $35, I decided to leave it alone.