I've created a simple tool to update ePubs (either one book or an entire directory structure) to make them easier to use with a Nook.
Specifically, it does the following:
* Tries to fix the ePub so the Nook can find the cover for the library view.
* Removes Calibre bookmarks.
* Splits HTML files at page break tags, to create a page break on the Nook (or on other ADE devices).
This program requires .NET 4.0. Source code is provided, under an MIT-style license, with apologies (I know I need to do some cleanup work, especially on the GUI).
Any feedback, unexpected errors, etc. are appreciated.
Downloads are available from the Google Code project