Happy Monday, Djcclarke!
Thanks for your post. It's important to be able to sync iBooks between iTunes and your iPad Pro. You're in the right place for help.
In this case, we have a resource that may help you through the process. Check it out here: Sync iBooks between your Mac and your iPhone, iPad, or iPod touch
If you're still running into trouble, be sure to reply to this thread. When replying, please identify the type of books you use with iBooks: were they purchased from the iTunes Store, are they PDF documents, or are they in another format?
Enjoy your week!