So, I took the bait and downloaded the update. It took an hour to get it running. I can see my books and all of my sideloaded books, files and videos on my micro SD card but when I try to run the videos I get the old cannot play video.
I created the mp4 files using dvdcatalyst and before the update they played just fine.
Sorry for the late reply,
Are you using N2A with your Nookcolor?