I also checked KB66616, but it just for ePO 4.5/4.6. It doesn't include ePO 4.0. And my case also needs to conside to upgrade ePO 4.0 on Windows 2003 to ePO 4.5 on Windows 2008.
Or, alternative upgrade approach:
1. P2V ePO 4.0 in Windows 2003 and in-palce upgrade to ePO 4.5
2. migrate ePO 4.5 on Windows 2003 32-bit VM to ePO 4.5 on Window 2008 64-bit VM, refering to KB71078
Anyone try to migrate ePO from Windows 2003 32bit to Windows 2008 64bit before? Does it work?
I've just realised I missed a point in your first message
You can use the method you describe - all you would need to do would be to make sure you export the agent-to-server keys from the ePO 4 server, and import them into the 4.5 server. That may be an easier option...