Much as I agree with not upgrading firmware without good reason.... You are very unlucky to get a failure. I have an S5 Controller here that I play with and have probably upgraded 20 or 30 times without problem, this includes loading all of the different S7 firmware versions onto it to have a quick look at what was in them.
You should be able to recover from the SD card with an image or if that fails you can connect a Terminal, although this requires taking off the BBB and soldering some connection pins and having a 3V TTL to USB converter.
Rich
Thanks for the suggestion, I have a 3v TTL to USB converter but no solder unfort. I do have an SD card however, will try just dropping the contents of the upgrade tar.gz onto a fat32 partition but in case that doesn't work do you have any advice on how to proceed?
Thanks