I can't be sure that Calibre was the cause of this - and no real damage has been done, since I had the files elsewhere...
I've just downloaded Calibre and installed it to see if I can get my head around using it to organise and reformat the books I have.
I plugged in the Cybook, and Calibre generated an error. Similar to
this one. I closed Calibre and restarted it, and this time it picked up the Cybook correctly, and read in the files on the Cybook (none) and on the SD card (600 or so books).
I thought I might as well empty the Cybook so I was starting fresh, and from there only put on books that were in a proper state. So I selected all of them and went for save to disk, and then specified a directory on my hard drive. It processed the request for about a minute and a half on the task manager, and then reported it was complete. No files appeared on the hard drive. I then repeated but instead selected the save to disk all in one folder. Same thing happened, and again no files on the disk.
Having Calibre send files to the Cybook would be nice, but it's not exactly required since I can do this using Windows explorer.
I then took the SD card out and put it in a card reader to copy all the files off... and then noticed that all the .txt files were 0KB in length. Every .txt file had been erased. Other formats were fine.
Since I last read one of the text files the only thing I've done is throw a rather large PDF file on the Cybook, which it didn't like and displayed blank pages. So I'm suspecting that something may have gone wrong with Calibre.
In any case I don't want to point any fingers around, but I thought I'd mention it in case there's some kind of glitch.
Edit : All .txt files are blank. As are all .prc files, and some (but not all) HTML files.
Edit 2 : It now looks more likely that it was Calibre, as when I first connected the Cybook it showed 1.6GB free on the card, it now shows 1.7GB on the card. I've done nothing else to the card other than copy all the files from it. So the files vanished between the point where I connected the Cybook and it showed on Calibre and when I disconnected and put the SD card into the card reader.