Laptop dies, has a virus, OBD wire comes loose or stray static electricity are all items that come to mind. An absent minded tech could turn the key off during the flash, but I don't see too many human error things that could come into play.

No matter, like Rick stated it is a documented problem but it is very rare. Same sort of problem happened on 6.0s and 6.4s. Hopefully they get you a new PCM and get her up and running soon.