I have an iPod touch 4th generation with iOS 6.1.6 and my MacBook has OS X 10.9.5 with iTunes 12. I have some books (epub) in iBooks, but I can't transfer them to iTunes nor synchronize them with my iPod.
In some cases, books/pfd's fail to sync with iTunes.
A common way to solve this is with a hard-reset of the iPod Touch. You can do so by pressing the home- and power button for 10-15 second. You can release the buttons once the iPod is shut down.
Preforming this reset will have no effect on your settings and data on the iPod.
When this does not help, iTunes normally gives an error. You could search the web with the error code or place it here. Mayby other people had the same error and figured out how to solve it.