I did a system update and now iTunes won't apply changes

Yesterday I ran a couple of updates on my iMac and this morning I tried to remove a couple of books off my iPhone and iTunes won't do it.  It lets me access the correct screen and deselect the books that I want to remove but when I hit apply it starts the sync process and the puts checks back in all the boxes of books I want removed.  In a related issue...Mail seems to be having a similar problem in that I delete a piece of mail and all of a sudden it shows back up in my inbox.  Anyone else having this issue or know how to solve it?

No, it is set up to only sync selected books.  But I even tried to just remove all books and not sync any and it won't let me do that. It always acts like it is syncing correctly, then all of a sudden all books I'm trying to remove get selected again. 
I have a total of 20 books. 9 books are on the phone. I am trying to remove all but one of them and then add one other that currently isn't on the phone. I tried removing the ones I don't want first and syncing with the intention of adding the one I want after the others are removed. It wouldn't remove them. I tried unchecking the box that tells it to sync the books at all and remove everything and when I hit sync it just reverts back to the checked box and the 9 original books.

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