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Yes - you can install ePO 4.6 separately on the Windows 2008 R2 server and run in parallel. Agents will report (managed) by only one ePO server at any given time. You can then slowly migrate all the agents to report to the new server by doing a forceinstall of the agent from the new server.
You however cannot upgrade the ePO 4.0 OS to windows 2008 R2 and still remain supported since 4.0 is not supported on Windows 2008 x64 and R2. However, ePO 4.0 supports Windows 2008 32 bit with ePO 4.0 Patch 3 onwards. Please refer to KB51569 for supported enviroments.