FWIW, the Nook is a pretty old device, and many people were... disappointed... in their software.
I have never had to reboot my Kindle to see new books, whether it was supposed to happen that way or not.
As for calibre, calibre creates its own duplicate copies for internal use, and leaves the originals untouched -- you can do what you want with those.
The exception is calibre's auto-add folder. Books will be deleted from the auto-add folder when added; if not, calibre wouldn't know which ones were already added!
