I had two SWUs (sorry, GPUs) that were originally transferred from UA to CO, and applied to a CO operated itinerary, including a flight operating 3/3. Both upgrades failed to clear, but the SWUs didn't come back. A call to the 1K number yesterday got someone within two minutes (promised 30 minute wait) and after 15 minutes on hold with the agent, the SWUs came back.

What I'm less clear about is why a miles+copay upgrade has been charged to my credit card, but the upgrade has not cleared.