In order to deploy apps to 3CX v12 you need the latest VAD. Check if your VAD shows the option "V12" for project properties. If it shows it, then you will not have problems to re-deploy any app.
Also, the backup will save your callflows and restore them in the new installation, so you should not worry about that, but in case you need to make changes to your apps, you should ensure that your VAD will work on v12. And if not, upgrade it.
Kind regards.