Originally Posted by stustaff
Yeh that all makes sense an I know its iTunes 'special' needs that are getting in the way here however at the moment I just drag a book from calibre into iTunes and this does not alter the original file stored in the calibre directory at all?
Be careful with this. Calibre thinks it owns the file and the directory structure that the book is in. If you change the title or the authors, the directory structure will change, making the iTunes reference invalid. From the iTunes perspective, the book just disappeared.
And no, this isn't an invitation to start yet another "Calibre should use my folder organization and not copy books" discussion.