Can I follow the instructions on http://arduino.cc/en/Hacking/Upgrading16U2Due, but use this avrdude command?
avrdude -p at90usb162 -F -P usb -c arduino -U flash:w:UNO-dfu_and_usbserial_combined.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
Is this likely to break anything further than it already has been? 