Thanks to the Ubuntu boot recovery program I was able to get back my bootable Ubuntu fairly easily. Although I had to cut a CD to do it as my original USB Ubuntu was 32 bit and my installed system 64 bit. The recovery tool would not repair a 64 bit system when running from 32. Booting the recovery CD normally did not work either, but safe mode did.

At least as an added bonus it detected and added a menu item for OpenIndiana although it detected it as Xen.