When using Collaboration Services and Migration Manager for AD together the two products should not touch the same objects at the same time.
Before migrating into the Collaboration Services stub objects with Migration Manager for AD the stub objects in the subscribing location needed to be removed from the scope of Collaboration Services.
If you do not remove the stub objects from scope of Collaboration Services before migrating into these objects with Migration Manager for AD than a Collaboration Services sync can overwrite the objects you have migrated into.
For a more detailed look at your specific configuration and deployment issues when using these two products together contact our Professional Services department for more information.