Using the public beta, when I updated to IOS 10 beta 4, I lost all of my PDF books in iBooks. Would not sync. After updating to public beta 5 today, iBooks still will not sync, or even recognize my iBook library on my iMac.
I had the same problem with my 6S plus on the first public beta. I deleted iBooks. Performed a hard reboot, and then downloaded iBooks again. It took a couple times, but it took and was able to access my PDF's. No problem since. But I am having a problem with notes between my IOS devices and my macs... #betalife