Are you using Bluetooth, or the steering wheel buttons to make changes to the CCF? I have always used the steering wheel buttons when messing around / uploading the CCF, I just feel better taking the somewhat finicky Bluetooth connection out of the equation... I figured it's one less thing that could go wrong during that very, very critical upload process.

I have never experienced an "incomplete CCF upload" message like you did, but since the change you made apparently stuck, my guess is that your Bluetooth connection - not the file upload itself - got interrupted during one of the multiple resets / reboots the car's electronic went through as part of the routine.