My music library will no longer sync.

I recently upgraded to IO6 and itunes 11.  Disaster.  Now my music library has disappeared from my ipod and a lot of old apps I want ahve appeared.
I have dleted the old apps, but despite the fact that i've got "Sync Entire Music Library " highlighted, my music library on the ipod remains empty and it just won't move across.   I had an error message saying my ipod needed to be restored to factory settings but that seems to have disappeared. I don't want to do that as I have some data in some apps which I need to keep.  What am I doing wrong?  Is there no longer enough space on my ipod??

I would backup the iPod
iOS: How to back up
Get all your synced media like apps and music in your iTunes library and then restore from backup.

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