Hopefully this solution will help someone in the future.
Turn off all Joeys with their Power button on the remote, stop all recordings and turn off the Hopper with the Power button on it's remote. Leave the TV on. You will see a screen something like press any button to turn Hopper on.
After a while the screen will change and you will see a screen showing guide downloading and a %. It only stays on for a short time and alternates with the turn on screen. After about 25 minutes it will get to 100%.
Then it is good to go.