They are no longer in iTunes.
Go to your user Library>Containers>com.apple.BKAgentService>Data>Documents>iBooks>Books
You will find your .epub files there. Unfortunately, Apple uses numeric codes for the titles, not the name of the book, so you will have to double click and open each one until you find the one you are looking for. If there is a faster way of doing this, I would love to know it.