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I have my ipad setup like yours, but I haven't had any problems. I upgraded to 8.3 yesterday and my transfers went fine after that, so I don't think that is the problem. Can you see the books in itunes itself?
I did have a problem a few weeks ago when suddenly the books were no longer in itunes, but calibre thought they were, so I used "remove books from matching device" (just so calibre "knew" what was going on) and then sent to itunes again and had no problem since.
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