I've put this up in a previous thread, but this is a classic bug which Apple has elected NOT to fix, not for several months, maybe not ever, and it's linked to the USB download of thousnads BOOKS only--music and videos will still download thousands of titles or a 100GB of data.
Here's my workaround post from another thread, and it still works:
I've had the same problem Syncing lots of books (about 3,000 in my case), and it always timed out at around 250. For me it's always the same number, almost like binary 256, which leads me to believe it's a software variable definition error. And yes, you can just keep hitting the sync button after the end of every "lap" to eventually get all of them.
Anyway, I did find a workaround that worked for my iPad: instead of syncing via USB, which is usually faster, try the Books sync using wi-fi (you must go through authorization and permissions with both computer and phone/tablet the first time). In that case, over a good N network router, the remaning 2,000 books all went on all at once fairly quickly. It's apparently a USB port time-out phenomena, so make sure your USB ports are not set in "power save" mode (the default in Windows 8.1--I don't know about Mac). But still, wireless may be best in this case, which is counterintuitive considering long wireless file transfers are usually less reliable the hard-wire. Funny how an older iPhone can take hours to sync 5,000 songs and not time-out, but just 3,000 books using a lot less data dies prematurely.
I just got an iPhone 6 Plus with 128 GB, and it worked for that as it did for my two 128GB ipads (both Air and Mini).
If you cannot or will not use wi-fi, must or insist on USB, you must just ...leave iTunes on and click Sync every few hours, including watching TV which is connected directly to PC graphics via HDMI. It's like the old days when you could only copy one folder at a time in DOS 1.0--think of it as 1980s retro-computing, like cassette tapes and scratchy vinyl.
And yes, you are all right that it's "shame on Apple" for not fixing this after about a year now. I'm a software/network engineer with 30 years experience, and it's a shame on our profession. Old school folks like me would never let such cocca persist.