Well, it's some sort of misunderstanding
I
have checked both the C: drive (to see if Calibre put anything there, as it should have, result is always negative) and the SD drive. I've checked the SD card in a card reader, on the Cybook itself, and on the Cybook connected to the PC. The file size is changed to 0KB for all the files in explorer, and a blank page on the Cybook.
I'm not
just checking through Calibre, in fact the only time I used Calibre to check if the file was gone was in the video to keep things simple.