First thing to realize is that the HD/+ do not expose a "disk" interface to the SD card when you connect over USB. The MTP protocol has the Nook itself reading the card when the computer makes a request.
As a result, there could be artifacts if the Nook catalogs the contents when the catd was inserted, removed, modified, and reinserted.
MTP protocol allows the Nook to stay active while on USB (devices with card reader modes essentially shut down while the computer sends commands directly to the card). Being active, the HD/+ MTP negotiates file access so that only one file at a time is transferred, so any inerruption in the transfer only affects that file, and the protocol can abort and clean up partial file -- instead of risking partial file and bad directories on the card if a cable were pulled during card reader mode on other devices (note how there is no "eject hardware" entry for the HD/+).
Personnally, I'd use a card reader to archive the contents, format the card IN the Nook, reboot the Nook to ensure the card is seen as empty, (maybe a second format after the reboot), and use MTP protocol to copy the stuff back to the Nook.