The load balancer should not show the second node in the farm as down but it is unrelated to this command.
This command only needs to be run when you're setting up the federated trust and not running the commands on the primary AD FS server. If you're doing the initial federation from the primary AD FS server, you do not need this command at all.
The farm will be managed from the primary node.
Check the simple stuff, make sure the services are running on the second node, check the event logs.
Then, from a workstation, create a host file entry for "sts.contoso.com" or whatever your AD FS name is and point it to the second node. Check if you can access and authenticate to the URL "sts.contoso.com/.../idpinitiatedsignon.aspx".