When it happened the couple times with my XL/Fractal Bot, it was always during the actual transfer process of the FW proceeded by a, "transfer error" as per Bot's window/notification.
Prior to Fractal Bot there were no check sums with other transfer utilities other than the AFX II's display after the transfer completed, (check sum error)(if memory serves me correctly) as it was a few years ago now. Lets just say that with the Axe (gen.I), I had the manual ROM boot procedure down pat and left only 4 screws fastening the cover with it the Axe unracked. That's how frequent it happened and the main reason I got the XL. I tried troubleshooting as best as I knew how with the obvious, (usb cables, using different SysEx utilities, closing all programs other than what was needed for the transfer, etc.)... just like clockwork, every other or third FW update it would bork. I don't think we never got any resolve from Fractal about these isolated anomalies.
And I'm sure that in some cases you are right when people have shut their Axe off before the install of the FW procedure had been fully complete. If that be the case... hopefully they'll learn.