iTunes deleted my Epub files

Unfortunately, when I was (only) trying to copy my epub files from iBooks to win10, iTunes deleted some epub files from the device ⚠

I was doing it by -> iTunes -> file -> device -> Transfer purchases from "device"

I have newest version of iTunes (64b, windows 10) and iPhone 4 (with actual iBooks, and iOS 7.1.2)

I was doing it only for backup, and iTunes deleted the most important files! I am so angry :/

How I could recover them? And how I could avoid that problem?

It was not the first time. At first I was trying to sync files via "sync your Books", but it also deleted some important epubs :/