Apple Configurator: Preserving Users Installed Apps
Preserve apps installed by a user who has checked out a device that is supervised by Apple Configurator. By default, whenever you connect a supervised device to Apple Configurator, any apps which were installed on that device by a user will be deleted.
By changing the setting described below, you can check out a device to a user, and if that user installs apps onto the device they will be preserved when you connect the device to Apple Configurator until you check the device back in.
1. Quit Apple Configurator
2. Execute the following command in Terminal:
defaults write com.apple.configurator PreserveUserAppsAndData -bool YES
Now, when you connect the device to Apple Configurator to update or apply new settings, any apps installed by the user will be preserved along with their data. When you check the device back in, the user-installed apps will be deleted.