I’ve been running OSX Yosemite since the first beta was released months ago. Typically for me to upload PDF files to my iPad, I would just connect the device, open it up in iTunes and just drag and drop onto my iPad. This appears to not work at all now for transferring epub/pdf to iPad.
I ended up finding out that you need to add the epub/pdf files to iBooks. But there’s a caveat.
If you have iTunes open, hoping to transfer the books to your device you won’t see them. You need to completely close iTunes and go back to the device’s ‘books’ section. You should now be able to click ‘Sync Books’ and choose your desired option of either sync’ing the entire library or just selected ones from the section below that (which should show the books you have available in iBooks).
Hope this helps. It was sure frustrating to me.