Apple Configurator - Updating to iOS 6.1.2 removed saved user data

We are currently managing several classroom sets of iPads using Apple Configurator. When updating to iOS 6.1.2 on the Supervise tab, about two-thirds of one classroom (about 20 iPads) and another 4 out of 6 in a special education classroom lost all previously saved data (application data, documents, pictures, etc.) during the update. We have another classroom that updated approximately 30 iPads following the same exact steps using the same configurator computer and none were erased so we're having a hard time figuring out the issue.
When I was watching the configurator run through the status updates during the iOS update (e.g. downloading iOS, decompressing iOS, installing iOS) there was another step on the iPads that lost data which was "supervising device." All of the iPads were already supervised so I don't know why this step occurred or what caused it to happen. With the grouping of 6 iPads, the 4 that were erased immediately started decompressing and installing iOS while the 2 that saved user data went to the downloading iOS stage first. I wasn't monitoring the grouping of 30 as closely, but I did notice the "supervising device" stage on the iPads that lost all user data.

I think for the teachers you are going to have to tell them to copy their data off the device.
Suggest dropbox or other cloud storage. Could set up a WebDave server.
A simple and popular way to copy files.
http://wiki.dropbox.com
Could set up sync-ing so they would come back in he fall. I'd be cautios and do everythig simple.
For syncing pc or mac folders to iPad applications.
"Using SugarSync, you simply designate folders that you want to “sync” to the cloud and it keeps everything in sync anytime you make changes. This is the way cloud storage should be done and especially if you are using your iPad for buisness or for school."
The only potential downside is that so many apps for the iPhone/iPad come with Dropbox sync built in which makes it extremely convenient.
http://www.tcgeeks.com/best-ipad-cloud-sync-app/
Doug says:
"This can be done with Dropbox as well using one of the many Dropbox addons…"
http://wiki.dropbox.com/DropboxAddons

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