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When a replica is synchronized, it should send new relationships for features and rows involved in the replica. When a two-way replica is created using the Create Replica Geoprocessing tool, it does not synchronize new relationships from many-to-many relationship classes. For example, when a new many-to-many relationship is added in the child replica geodatabase, it is not applied to the parent replica on synchronization.
This is a known issue.
If a two-way replica that includes many-to-many relationship classes needs to be created, use the Create Replica wizard in ArcMap. Two-way replicas made with this wizard successfully synchronize the replicas, so that changes made to many-to-many relationship class tables in the child replica appear in the parent replica geodatabase.
The Create Replica wizard is located on the Distributed Geodatabase toolbar in ArcMap. For more information about the Create Replica wizard see Creating Replicas.