There are 15 pages on this topic so I haven't read the whole thread. Apologies if this is a dupe!
Many of my files that had copied to my 4S and were now refusing to copy to my 6 were fan-generated audiobooks (we call it podfic.) They had copied before, they were not copying now! After finding out that the problems appear to be related to ownership issues, and knowing that m4b is a protected format, I tried picking a single audiobook and changing it's extension to m4a instead of m4b. Then I re-synched and boom, it appeared on my phone! Obviously this may not work if the files are genuinely copyrighted, but if it's just that the file creator chose to use m4b, you may be able to batch rename your files. Especially with audiobooks. It did work for me. 🙂
By the way, I used NameChanger, a free tool, to bulk change my file extensions to m4a. I also backed up all of the files before batch renaming them in case it all went horribly wrong (never hurts to be careful), and I have iTunes set to keep my library in synch with my files.