Epubs get deleted after syncing

I'm using iTunes 12.2.1.16 for Windows and while syncing with my iPad 3 (using iOS9 second beta) my epubs after copied to the device get deleted. For example I have this biography wich I downloaded somewhere else and I have it on my iTunes library, it is checked and ready to sync, while syncing it is transferred to the ipad, but after the copy is completed it gets deleted on my device in the iBooks application. This only happens with non iTunes Store books. I have tried changing a few settings on iTunes and iPad but nothing seems to work. Please help.