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On the right-click menu for Remove books, there are various options to remove the associated formats for a book entry. If you do that, you will be left with what is known as an "Empty book", which is a perfectly valid way to keep a catalog of books without having an associated ebook for them. You can search and catalog them, you obviously can't actually launch from calibre to read them though. People frequently use such entries for wishlist items, keeping track of paper books they own etc. You can manually add more empty books using ctrl+shift+E or the Add dropdown menu.
Do *not* however go into the calibre folders and delete books from there manually - use that Remove menu within the calibre applciation to do it so that calibre's database is kept in sync.
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