There are several ways to migrate. Are you using the 'transfer' feature'? Are you deploying a McAfee Agent from the new server to a client that has been previously managed by your former ePO server? If you are using the transfer feature, it isn't a 100% when removing it's original location. In the second example you would need to remove the system from the old ePO server when you know that you are currently managing it on the new Server. Let me know and I will add some thoughts.
I plan on using the 'transfer' feature. It seems the easiest solution to me. It was my understanding that the agent would then point to the new ePO server.