It might be a problem with the SD Card.
When you connect your Nook to the PC it reads the NOOK hard drive and the SD Card as separate drives. If it's not recognizing the SD Card then it has something to do with the SD Card.
You can do the following:
1) Plug in your Nook. Go to Computer > control Panel > Hardware & Sounds > Device Manager. Then right click on the computer line item and choose 'Scan for Hardware changes'.
See if this brings it up.
2) Take out SD Card and put it back in while Nook is plugged in.
3) Check what happens when you try SD Card via a SD Card reader.
4) Try a restart of Nook (even though it's very unlikely to be Nook related).
5) Restart Pc.
For me I've gotten this issue just once and it went away by itself.
It has to be something with this particular PC - although it used to read the SD card. My home PC can still read it. Any ideas?