I’ve gotten several emails from people who “lost” a number of ebooks after updating to OS X 10.9 Mavericks. I had pointed out that iBooks moves ebooks from your iTunes Media folder to a hard-to-find folder, but in same cases, people’s ebook libraries weren’t migrated completely.
If this has happened to you, launch the App Store app to update to iBooks 1.0.1. Launch iBooks, then choose File > Move Books from iTunes. The iBooks window will show a progress bar, then tell you that it has moved all your ebooks.
You should now see all your ebooks in the iBooks app.