I don't know if this will work or not as I've never had this problem.
Install NickelMenu and in the config file in the .adds\nm directory, all the following line.
Code:
menu_item :main :Import books :nickel_misc :rescan_books_full
From the NickelMenu menu, execute this and see if that helps.
Another thing to try is in calibre, make sure you have Kobo Utilities installed. Then use that to check if the database is corrupt.
What firmware version are you running?