sf4dfish...what I would have done (and have done when this happens with Confirmed Region 1s) would be to just walk up to the RCC agent and tell them what happened, have them off-load me and then re-check me in correctly. The off-loading automatically returns your E-Upgrade to your bank. Calling Mileage Plus or Customer Relations can be a pain and can often take time and/or supervisor. And if the RCC agent wants proof of your handing over paper like you claim, they can simply call whoever checked you in (they can tell on the ticket and/or on the computer).

Although I'm not certain you could do it this way if you have checked luggage.

Also, I always recommend that you make a photocopy of any paper certificates before you hand them in, just in case you need the cert number or anything after-the-fact to support what you handed over at another location. I always write the date and flight number on this photocopy, as well.