After update, bunch of non existing devices where added.
I had to go through each site that I updated and delete all non-valid controllers from the tree and then did a full scan. Hopefully this corrected the issue.
You can clean up the T3000 tree by going to Database → All nodes → delete offline. I am not fully following why this is suddenly necessary but if you do find yourself with fluff and garbage in the T3000 tree its easy to clean them out:
Deleting offline is not the way to go, because you need to check if all devices actually connected is online. I guess devices from your test environment got into update.