I tried disconnecting the Ethernet cable from the box and restarting it. Now both the old and the new boxes show up with an ! symbol, but give different errors. If I press OK on the replacement box, I get a C423 error and an option to remove the box. The phantom old box gives a V106 error and no option to remove it.
When the ethernet cable is connected, I can play shows from the replacement TiVo box just fine. Should I try powering up the old box and connecting it to my network to try and remove the phantom entry? I doubt the box would start up now that it's been deactivated though.