The same thing happened to me doing the 4.6 update installed using a USB flash drive. It didn't automatically reboot (although stated complete). None of the buttons on the unit worked. I unplugged the USB drive, nothing happened. I shut off my car, nothing happened (the unit stayed on and was basically frozen). I had to unplug my car battery, wait 5 minutes then turned my car back on. The HU started normally again but the version still states its 4.0.
Thanks for the tip from Clandest1ne.. I will try it again but next time i'll use an SD card.