Exactly the same way i did it when upgrading from EPO 4.5 to 4.6. Just deploy the agent from the new EPO server. The machines didn't get removed from the old EPO server they just stopped reporting to it. I just manually deleted machines from the old server when i seen them reporting to the new one.
My only hurdle was 200 machines at 13 sites at the end of a low bandwidth WAN and a few legacy Win2k machines that i needed to manage. The 4.6 agent won't install on Win2K so it's just a case of using the 4.0 agent and importing the site list and server keys.
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Additionally you can register the new ePO 4.6 within your ePO 4.5, import the security keys and then use the "Transfer system" action to tell any 4.5.x agent to contact your new ePO server ...