Controlling the Syncing of iTunes to iPad

I have e-books that I store on an external HD and use iTunes to sync them to my iPad.
Once I have them in my iPad I don't need them in iTunes anymore - so I delete them in iTunes - I want to free up this disk space (I don't read these ebooks on my MacBook.
How can I set iTunes that it doesn't update from my iPad all the ebooks I deleted in iTunes whenever I connect my iPad to my Macbook?
Any ideas welcome.

I managed to recover the files from the iPad by getting a piece of software to copy them from the iPad but this is far from ideal - is this going to happen again? Do I have to backup everytime I make a purchase just to be sure iTunes isn't going to decide to delete it?

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