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I'm glad you got things working right. That sounds like that was the problem -- you had dupes of the same book and when you switched the location of CC's default folder into the same one where the first books were, it caused some conflict. If you just import via CC in the future everything should be fine.
BTW, the default directory for CC is "mnt/sdcard" but on the Nook HD, that is actually the internal built-in memory! For some reason, B&N saw fit to call that "sdcard." If you ever need to put in the path for the micro sd card, you need to put in "mnt/ext_sdcard" which is where I now have CC putting my books.
--Pat
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