Your Nook Color Options: Root & ROMs
Did the update address your original problem? I know the old workaround for the stock NC's lack of a file manager was to install one of the Office apps from B&N's market, which had a file manager built in. That should at least allow you to delete. If you root or run a custom ROM, there are tons of Android apps like Evernote or Read It Later that are designed to manage reading lists built from websites.