Originally Posted by PeterT
Step 1: Don't open the book in Calibre's eBook viewer.
Step 2: Use the Tweak Book Calibre plugin. Explode the book, then go into the META-INF directory and drop the calibre_bookmarks.txt file and then rebuild the book.
In Calibre's viewer, you can turn off page tracking and thus, it won't add any files to your ePub.