I'm in the "minority" too. I find that calibre is a better way to organize and find books, so I try to keep the reader clutter free. Now if there was a way to stick books on the reader yet hide them from the ereader's software, I'd do that to maintain a backup.

(Also, my entire collection of ebooks is rather small. I'd rather let Project Gutenberg manage my library of public domain books and there is no point in keeping expired library books. The number of books that I actually purchase is relatively small.)