I don't think this is a "known issue." I do not have any trouble in this area, so unfortunately, I think it is unique to your setup.
One question - does Calibre think that the PC lib and the Nook lib are in synch? - i.e. when you look at the Nook with Calibre, if I remember correctly it puts a check beside books that are in both places, or some other indicator. From what you are describing, from Calibre's point of view, everything is correct, right? I'm just asking for background.
If the above is true, maybe you could try deleting the Nook books using Calibre and then getting Calibre to resend the books, although somehow I'll bet you've already tried that.
One thing you could do is transfer the ebook files manually (with Windows Explorer), from the Calibre library to the Nook. If you do this, you do not need to send the entire subdirectory but just the epub files themselves. I'll bet that makes the ebooks appear in the Nook's My Documents on the Nook display. This will allow you to at least read them on the Nook, although it doesn't solve your problem with using Calibre as your organizer.
Last edited by RAH; 02-13-2011 at 07:40 AM.
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