Did you update your Color Nook software to 1.2.0?
If not, you may have had the software automatically download and install itself. After that it restarts and you have to re-register it and download the books you have purchased through B&N.
I keep any side loaded items on the micro SD card, that I load form my PC and keep a copy of the loaded files on the PC.
Same thing happened on my nook 1st edition! I have about 900 books / documents in it! Lost all my files, shelfs even the firmware version was reset to version 1.5! Very, very disappointed, I want to break my nook to pieces!