What the command reported seems most likely an index corruption, you could try the solution posted here on stackoverflow: sqlite - How to recover a corrupt SQLite3 database? - Stack Overflow
This is what I see as the simple thing you can try, other than that, there is manual editing and checking for corruption that could result in a really huge waste of time.
If you are going to start from scratch, please be sure to do daily or weekly backups of your server, it is as easy as adding a line to the /etc/crontab file (on Linux) that will create a .zip archive of the specified file or folder. Here is how you do it (check also the answer): zip - Simple Cronjob to backup a directory - Stack Overflow
