Rather than start a new thread, since I have a similar and very strange problem.
My iBooks are not syncing properly on my iPad Air 2.
I get the book, yet there is only half the book downloaded.
Edit: I figured out what the problem was. For some odd reason, when you buy a book in iBooks.
Your iPhone version is different than the iPad version.
Probably due to screen size difference. So you're getting twice to almost 3 times the pages on the iPhone, as opposed to the iPad.
But the whole book is being downloaded, it just seems a bit odd to me.
When I was using the Kindle, the book pages were the same for whatever device you were using.