Turn off in the Preferences, When a Supervised Device is Connected: Automatically Refresh. This is the first thing to make sure of before hooking them up at all. Or it WILL auto-refresh them.
I tested this on 3 carts of iPads, hooking up 30 at a time, and none of them auto-refreshed even though it said Waiting for Connection. I was able to select new apps that needed installed and install iOS 6 and none of the iPads lost their data or settings(Wifi settings, DNS, and Restrictions). The one thing to ABSOLUTELY check before you click Apply is to make sure you do not restore a back up or change the iPads name. Restoring a backup that says Multiple or a previous stock "image" of the iPad will erase certain settings and all saved data. There's an option for Don't Restore Backup. The first time I hooked them up the Backup setting was set to Multiple. Very bad things would've happened if I hadn't noticed that.
I hope this helps alleviate any problems you others are having. I kinda answered my own question but thanks for the interest.
We have an extra iPad for IT testing and I was able to test before I plugged in a cart. I suggest you do the same if possible.
EDIT: I would like to add these were all Supervised Devices. I have no idea the difference in what would happen if they hadn't been.