You have to reprogram everything. Settings are stored in the head units, not the modules.
MyReef was supposed to include a "backup" feature, but this still hasn't been implemented yet. Even though DA is calling this latest release 'production' and no longer beta, it still has bugs and features missing.
I wouldn't hold my breath waiting for DA to activate the backup/maintenance features in myReef anytime soon. I have a sneaking suspicion that button on myReef is just an image placed there, and they haven't even begun to program those functions yet. You are just going to have to re-program everything once you get the new headunit.
Hope this helps,
Landon