Alright, so I got this message a few days ago when messing around with ZeroNet (a lot).
Well, that doesn't look too good. I messed up content.db somehow. I tried to fix it with no success, and in the end I gave up and setup ZeroNet again. I backed up my data folder and let ZeroNet run again. (I kept the important files like the keys and users.json) Then, I went back to the websites I commonly look at so I can seed them again, went onto WhiteHub, and made a long post complaining about losing my sites.
It gets worse. After going through the effort of updating the NameCoin domain, and setting everything up on the new sites, I remembered the private keys to the sites are in users.json. I didn't lose my sites... I was just a moron.
The moral of this ~~rant~~ story is to back up content.db, especially if you like to mess with ZeroNet as much as I do. ;-)