You can redownload your iTunes purchases by:
I suspect that iTunes was signed into the alternate account on the computer on which you did the update.
You might be ablt to restore from back with all the iTunes purchases being in the iTunes library and iTunes singed into the correct account and get your information back. Go to iTunes>Preferences>Devices and look at the date of the backup(s) you want one date at the time the iPod was connect when yo did the update or earlier.
I have a similar issue happenning with my ipod touch 64GB running IOS 6.0.1. My music content is stored via itunes on my Snow Leopard macbook pro as well (and not in the cloud). The music on my ipod (which is sync'd to my macbook pro when I connect via usb) has randomly disappeared about 3 or 4 times lately, not during sync'ing and unrelated to battery charge levels. Fortunately I have been able to restore it by restarting my macbook pro then re-syncing the ipod, which it is now doing as I write, but it takes hours (for over 3000 songs). Having looked at a few other forum discussion pages, it seems this may be a bug related to IOS 6 updates and using music/itunes and podcast playing apps. The same thing has intermittently occurred with some other content such as downloaded podcasts, iplayer content and photos. Once I reconnected the ipod it synced and apparently restored the content, but I can't understand why it lost it in the first place, and its very annoying. Lets hope the reinstalling works on my ipod tonight....up to 248 of 3326 songs syncing as I write....