How are you loading books on to your reader? If you're using either the Sony Software or Calibre, when you transfer a copy of your book to the reader, there should still be a copy kept on your computer. So you shouldn't have to worry about copying books back over.
Now, if you're using the sync function of the Sony Software, I'm not sure what happens when you delete a book from your reader--don't know if this will also delete it from your library or not. (Hopefully someone who uses the sync function of the Sony software can clarify this.)
dordale