Hi,
most probably you are not using the correct workflow template for changing the hierarchy. IDoc based replication of a hierarchy change requires that MDG sends two IDocs: one for the hierarchy, one for updating the master data. This is due to the fact that the standard ALE inbound for hierarchies updates only the hierarchy but not the master data. This inbound does not belong to MDG, so we cannot change the same. As mentioned by Kiran, the behavior of the SOA replication is a different one. In that case the inbound belongs to MDG so that we can update both the hierarchy and the master data with a single message.
Please refer to the MDG-F configuration guide, section workflow templates for more details.
Best regards
Michael