if you sure the problem is with database sqlite file and your data is not 
corrupted (integrity checked database = OK)
just an idea why not extract your data and put it on new database (sqlite 
or another dbms (recommended using export_to_csv_file() and 
import_from_csv_file() )
*# backup database*
sqlite3 ~/web2py/applications/app/databases/app.sqlite .dump > ~/app.bak
*# restore database*
mv ~/web2py/applications/app/databases/app.sqlite 
~/web2py/applications/app/databases/app.sqlite.old
sqlite3 ~/web2py/applications/app/databases/app.sqlite < ~/app.bak

another way is using web2py export_to_csv_file() then import_from_csv_file()

*ref:*
http://web2py.com/books/default/chapter/29/06/the-database-abstraction-layer#Exporting-and-importing-data

best regards,
stifan

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