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With the NST when you eject it, after calibre say the device is safe to remove, you have to wait for the nook to finish updating, with a large number of books wait two to three minutes to disconnect to the cable.
My experience is that the NST does not like to have large numbers of books loaded at a time try with ten at a time disconnecting with each transfer.
If this is a new sd card then use a card reader to transfer the books using connect to folder in calibre, then install the card into the nook.
bernie
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