I don't know if this will help or not, but to remove Supervised devices that have a "Waiting for connection" status in Apple Configurator (like if the device was lost or stolen) you can remove it from the list by holding down the Option key and right click (or control + click) on the lost/stolen iPad. You will see an option listed when you hold the Option key down that will say *Remove*. Choose Remove and it'll go away from the list. Maybe try removing it and re-supervising?
Hope this helps.
I will definitely give that a shot, but two things. Does this retrieve VPP app codes that were tied to that device and when I prepare the device won't it get wiped anyway? I'm trying to undo this, so that these students don't lose the info on the iPads. Thanks.
EDIT: I just tried on one that was stolen, and it did not put the app codes back into the app section, so unfortunately this will not be an option for me, but thank you.