[galligaskins]

I can contribute a bit more information:

I have been having very similar problems with my iPad and iPhone sync, so I removed the entire calibre library from iTunes, then connected calibre to iTunes using the Share button and transferred the entire library to iTunes (no device was connected, but the Apple device plugin was enabled). I then connected my iPhone for a routine sync, and immediately saw almost all the calibre library disappear from iTunes. The few books that remained (with one exception) were all marked with an ! sign, indicating that the entry remained in iTunes but the file itself was missing. I repeated these steps with the plugin diabled, and the iTunes library remained intact.

I would add that calibre does not detect that a book is already in iTunes when transferring, so multiple entries can appear in the iTunes book list for each book; whether this indicates multiple files, I don't know, but I suspect so.

Regards

-gallygaskins-