I posted in the Calibre forum (https://www.mobileread.com/forums/showthread.php?t=85226
) but you may have missed it.
I have released a plugin for calibre that will allow you to view and delete any books on the device (free, pdf or epub). The details are in the link above. Beware that you must have the 0.6.95 version of calibre.
If it gets some testing it might get into the an upcoming release. Read the details from the link above. I would be interested in hearing of issues.