If it's already cloned and flash.. uninstall install-tools and install bootmenu.deb .. that will recreate your boot menu and let you boot to your install SD and you can update the new SSU there.

Read my post in the Diablo Update thread.. I had no problems loading the SSU to the internal Diablo, rebooted (lost the boot menu and so went to flash), installed the SSU on the flash, rebooted, and then installed Bootmenu and got back into internal SD.. no data loss and both diablo's were updated.