How did you delete the PDF formats- through the GUI/the CLI tools or by directly deleting them from the library directory tree? If the latter, you'll need to do a library check (click the downward arrow to the right of the library symbol in the toolbar and open the library maintenance submenu), Calibre doesn't pick up changes you do in the library directory tree. You should only interface with your library by using either the GUI or the CLI tools.
Edit:
Moderator Notice
Moved to the appropriate subforum, as well.