TI tried to flash the rom manually but failed miserably (ran into this: http://forums.androidcentral.com/google-nexus-7-2012-rooting-roms-hacks/307466-how-recover-nexus-7-2012-bootloader-fail.htmlthis page). I
I decided to use the Nexus Root Toolkit (http://www.wugfresh.com/download here) to go back to stock Android 5.1 (losing everything on the device of course). That worked like a charm and re-rooting it afterwards was simple enough Rooting guide for 5.1.1. In
In the past whenever a new Android version came out I had to flash back to stock Android to get the update and then re-root it. I'm sure some people manage to update without erasing everything...