Resolution
What do I need to do before decommissioning the source Exchange 5.5 site in an Exchange 5.5 intra-org migration?
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Exchange Migrator 1.x
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Exchange Migrator 2.x
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It is highly recommend that you take the source server off line for a day or two, to make sure everything is still working as desired, then at that point you may decide when to actually decommission the server. If you need to leave the source system in place, you should be able to just delete the source mailboxes. Please ensure that mail routing is in order (i.e. MX records etc.) and you have a backup before continuing. After ensuring all objects have been migrated off the server and your sure the post migration steps have been performed to update mailboxes, permissions, and Public Folders, follow the Microsoft recommendations for decommissioning your source servers.
XADM: How to Remove the First Exchange Server in a Site (Q15259)
XADM: How to Delete a Server from a Site (Q189286)