Altboot is loading the software from a USB key, but there is formatting involved, it wipes the device when it is done.
But, I have been told I cannot give the information out here, while I can freely give that information out over the phone, it is against the rules to do the same thing here on the forum.
Try applying the patch and see if it resolves the issue, I think it won't though, it is a patch that needed to be installed previous to the update. I don't have a 56xx machine to replicate with here by doing an altboot to an older firmware and then straight upgrade without patching to current and setup scan to server 2012.