By making Calibre see the memory card as the storage in a Nook, I hoped to avoid any loss of tagging information or other unforseen syncing/transfer issues. Caution is prudent when you're dealing with nearly 4700 ebooks.
I don't like the thought of waiting for them all to sync only to find out that the tagging info doesn't work or storage format isn't valid for the Nook.
I've done as you suggested and Calibre is getting the info from the card... slowly..
At this rate it'll take an hour just tell me whats on the card and what isn't. Oy vey