I also found these errors after upgrading from 11.1
I have recovered my deployment.
I found the issue was
arcgisserver\config-store\machines\<servername>.<domain>.json
And
arcgisserver\config-store\version.json
were both corrupted.
I stopped the ArcGIS Server service and copied these files in from another similarly configured ArcGIS Server deployment and then renamed / configured the files appropriately for the server with the issue, then restarted the ArcGIS Server instance.