It have never yet worked for me, but in theory, if non vital parts are wrong, then you can try to use sqlite3 to open the database, and save what it can. Under windows I made the following very simple .bat:
echo .dump | sqlite3 KoboReader.sqlite > KoboReader.dump
move KoboReader.sqlite KoboReader.bak.sqlite
echo .quit | sqlite3 -init KoboReader.dump KoboReader.sqlite
(Before using it the .bat file and the KoboReader.sqlite should be in the same folder.)
In theory, this should work, in practice never worked for me (library lost, tiles from the main screen lost.)
There is a more developed version at
http://timlegge.blogspot.hu/2011/03/...-database.html. I just found it as I searched for the linux script I found earlier. This solution seems better.
(BTW after loading books from calibre there was no problem, but after doing several EPUB highlights and comments, I had many database errors.)