If you do not perform the following step, ArcGIS Server services and hosted services published by portal users continue to run on the server.
If you no longer want ArcGIS Server services to be available to any application, log in to ArcGIS Server Manager and delete the services. Hosted services published by portal users are located in the Hosted folder.
The services should start working once you re-federate and add the hosting server.
Reference: Removing an ArcGIS Server site from your portal
Not sure about the apps though. You might like to refer ArcGIS Enterprise backups
Think Location