Yes, it is possible to unfederate an inaccessible ArcGIS server from the federated servers list in Portal for ArcGIS. In the event an ArcGIS Server is no longer accessible and cannot be restarted, the server can be manually removed from the federated server's list of Portal for ArcGIS.
During the standard unfederation process, the Portal Admin API is required to communicate with the ArcGIS Server Admin API. If ArcGIS Server is down, communication is not possible as ArcGIS Server Admin API is unavailable.
To manually unregister an inaccessible ArcGIS Server from ArcGIS Portal Directory, follow the steps below.