ProChargerTECH, thanks for your input. As I said in my initial post regarding Diablo "it is not necessarily something they are doing wrong", but what they are doing is causing problems with our reflash routines.
When EFILive reflashes a controller that uses our own bootloader we do a flash validation check right at the end. So just before the flash is finalised our bootloader goes and validates the data that was written by comparing to the checksums in the tune, if everything is good then the flash is finalised and the ECM is allowed to reboot in to a 100% functional state, this is a safety net to ensure a half flashed ECM can never reboot and attempt to run an engine.
If Diablo didn't put in the extra data at the end of the segments to correct the CVN back to stock then there would be no issues for us, however they do and people are going to keep running in to this issue. At this point what we may do is add the ability to detect and remove the CVN correction bytes on their tunes.

Also, the tune we were sent in, I am making the assumption that vehicle was only tuned with a Diablo, this may in fact be another tuner doing this.