Resolution
The Cisco Unity Message Repository (UMR), which is built into Cisco Unity 3.x and later, allows outside callers to leave messages when the primary Microsoft Exchange server is offline. Messages are temporarily stored on the Cisco Unity server in the \CommServer\unityMta directory and can be accessed through a special UMR conversation. When the primary Exchange server comes back online, Cisco Unity begins to pass the messages as normal into the correct message store.
In order to recover the messages in the Cisco Unity MTA failed folder, move these messages manually to the Cisco Unity MTA folder, and then restart the UMR sync service.
Refer to Cisco Unity: Defining the Unity Message Repository for more information.