MTA messages are accessed by a special UMR conversation while the primary Exchange server is offline. When Exchange comes back online, Unity should attempt to deliver those messages to the user's Exchange mailboxes. If that doesn't happen, you can restart the MTA service which should trigger delivery. Here is a link on UMR that might be helpful to you:
http://www.cisco.com/en/US/products/sw/voicesw/ps2237/products_tech_note09186a00800949fa.shtml
Hailey
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