If you are on a new PC and have just installed Calibre, Calibre has not built its database yet, so you won't see any books in its Library, either for the PC or the device, I should think.
So, it seems you need to re-add the books to it. If I were you, I'd copy all your books from the Nook to the PC using Windows explorer into some temporary directory. Then add the books to Calibre. At that point, it may notice that the PC and Nook are in synch, but maybe not. You might have to then delete the books from the Nook (with Windows Explorer) and then send them to the Nook using Calibre to get it to know about them on the device.
I haven't tried any of this, but this is the way it seems to be broken to me, just thinking about it and how Calibre works.
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