Are you actually on a Mac or Linux machine? If that is the case you can pretty much copy/paste this into the Terminal:
Code:
echo ".dump" | sqlite3 /Volumes/READER/Sony_Reader/database/books.db | sqlite3 ~/Desktop/books.db
cp ~/Desktop/books.db /Volumes/READER/Sony_Reader/database/books.db
That will recreate the DB and put it back onto the Reader (assuming you have no SD card as well). I'm not familiar with SQLite on Windows to know how to repair it through cmd.exe.