macOS Sierra, Multiple problems with iBooks syncing to iTunes 12
I would download Calibre to edit the metadata before adding the file saved by calibre to Books.
Also, I've found that unchecking ibooks in system preferences>icloud>icloud drive on my mac fixed the issue with itunes, and I only really read books on my iPad/iPhone, and having Books turned on under icloud on those devices' settings doesn't seem to mess anything up so this works for me.