That TNT file loaded fine for me in 4.121 on XP. Plus it enticed me to visit your site and download your books as well!
For the deleted files, I think (?) Calibre is just deleting its own database copy, so the original files should still be wherever you added them from. As far as the new EPUB files, can you just pull them back off the device? I know you can pull lrfs from the PRS-505, but I remember the ebookwise exploded imps once they were added, so I guess it depends on the device.