Have you disabled the Apple App Store on the users that have received the apps with device based licensing?
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I re-read your request and in order for device licensed apps to update, the AM server would actually have to do this job. You can do this manually right now by issuing a manual "Install Application" command to your devices. Be advised, though, that we know of a current issue with iOS 9.2 and this use case where if device licensed apps are updated in this manner, this could prevent the app from launching in the future. The workaround, at this time, is to remove and re-install the app.
So, if you are not running iOS 9.2, you can issue the "Install Application" command to get your apps updated. In a future release, we will handle this in an automated fashion. If you are running iOS 9.2, my advise would be to avoid upgrading your device licensed apps until an iOS update is released to fix this issue.