I doubt the Cypher is at fault here. My guess is that this has to do with the state of your store before and after the upgrade, so information about your upgrade process would be helpful (order of steps especially with regard to backup and restore with respect to when the upgrade was performed), and if you're able to share your store file that would also help.
Also was a consistency check run before the upgrade?
You seem to be running Enterprise version, do you have a support account with us? If so creating a support ticket would be the recommended way to get immediate enterprise support.