Hi Randy,
Sounds like theres couple of issues at hand here. I would like to start of with the original Portal-Server configurations you had before, If you can tell us more about that, it would help here:
1. Was Server and Portal Federated? is Arcgis Datastore in the picture as well?
2. Are they on the same or different machine?
3. Do you have a system diagram that you can share?
and from there, tell us if you are still using the same Server site (config store and directories) or are you creating a brand new site? Based on what you mentioned above, If you are "upgrading" the Arcgis Server component, then you should see "Continue Upgrade" rather than "Create new site" or "Join Existing Site". The error mentioned there, simply says it cannot recognize that account you entered for that particular site. or its the wrong username and password.
The join existing site feature only come into place if you have a multi-Arcgis Server machines. In that situation, you would need to upgrade the hosted server first, then sequentially, upgrade your other Arcgis Servers.
Upgrade ArcGIS Server—Deploy | ArcGIS Enterprise
I realize that these questions might already been asked through the case. but I just thought I'd ask again just for the visibility of this thread.
Thanks,
Harrold.
