1) I guess the old server should not be available (epo services down would be enough I guess) once the new server is online or doesn't it matter in this scenario? Or can they co-exist so that you can update the agent in phases?
2) You tell me to rollout the new agent or the new sitelist.xml. I guess you mean just replacing the existing sitelist.xml on the clients with one from the server? Which file will that be on the server? I think there's more then one... I think replacing files on the clients is easier then rolling out a new agent, right?