Question: Are you sure calibre is using the right library folder? (Perhaps it got switched?) You can check the current library folder from the Switch/Create Library dialog (above).
If the database got mangled (calibre is using the right library with all the book files):
- First, copy your library to a backup folder. (Backups are always good.)
- Then, run Library Maintenance ==> Restore Database.
It should rebuild your library based on the actual files in it. Hopefully that will fix it.