This happened with the most recent update. I tried reinstalling iTunes and shutting down phone without success. My audiobooks are downloads from public library as MP3s.
Learned the convoluted and frustrating methods to make them be audiobooks rather than music and to not shuffle the chapters with "Get Info" and they are still listed in my iTunes library. Most of my music is from my own CDs.
I can get 1-2 audiobooks to download at a time if delete everything supposedly on my phone in iTunes then add to the iPhone's playlist again. If I add another book or album it deletes the previous ones.