You have a problem then I am afraid as there is no supported way to copy books back off the iPad.
What software are you using on the iPad? You may find that the "iPhone Backup Extractor" software can get your books out of an iTunes backup, but whether it will succeed probably depends on the app storing the books. The free edition can be used to test if this will work for you, although if you have a lot of books to recover it might be worth forking out the registration fee.
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