[Sirtel]

Never, ever delete files from the library directory. You can't "re-scan" the library and the result will be a corrupted database. If you don't want those books in your library, either remove them via the Calibre GUI (Remove Books) or move them to another library, as Jon suggested.

What I do is tag the books as read and color the library entry red. I don't remove them from my library, as I often reread. If I never reread, I'd probably create a virtual library for finished books.