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Pat, you should probably also keep the folders where CC puts its books and where the Nook downloads B&N books to separate, or you may encounter this problem again, particularly for books that are also in the B&N cloud.
The books that CC import always show up in the library where books from B&N show up in -- even if you keep the CC-imported books on your micro SD card -- so you don't have to worry about that.
--Pat
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