I feel you on this one! I thought I had bricked my Nook last night when the same thing happened to me. I could boot up but always ended up in Clockwork without any way of getting past it. I decided to restore it to stock, following these directions:
http://forum.androidcentral.com/bar...5414-how-restore-nook-color-rooted-stock.html
FYI, I misread the title and thought it was going back to virgin stock. Since this method returns the Nook to rooted stock, that may be why I had a problem installing Nook update 1.1.0 and I couldn't use my Froyo and HC SD cards. After repeatedly trying the 8 interrupted boots method, I decided to try using the Hardware Key Combination method to do a factory reset. It worked and I was then able to successfully install the update. I am now running Froyo and HC again!
HTH