Part of the challenge you may run into is that if the WA creates the "public" or "frontend" URL for you, (the URL clients use to reach the Portal and the URL), then it's stored in all items and within the federated server. If your new server has a different FQDN and you move the WA onto it so you can register with Portal, you'll need to handle the new URLs in all data. If it's a new machine but has the same CNAME, then you just need to make sure you use the same URL to register the WA and you'll be fine.
