I would like to move to native mode on both of these, but I'm not sure what sequence to use -- Windows first, then Exchange Server? Is there anything I need to do first? There was never any Exchange 5.5 or lower servers on this network. We are planning an upgrade to Windows 2003, then a Move Mailbox install of Exchange 2007 in the near future.
In Exchange 2003, the following features will require you to maintain an instance of Exchange 2003 in the organization:
The process of moving or transitioning from Exchange 2000 to 2007 does not support an in-place upgrade. If you consider that Exchange 2000 was not 64-bit, the notion of an in-place upgrade not being an option becomes more obvious. That being said, there is a useful Microsoft TechNet article, Best practices for transitioning an Exchange organization, that goes through some best practices for transitioning to Exchange 2007. You will most likely use the Move-Mailbox cmdlet or the Move Mailbox Wizard.
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