More about VMR (Search SDN u will find lots of articles on the same):
Edited - Try with this kind of Message format for updating messages (Delete old value and then insert new one)
<ns0:ValueMappingReplication xmlns:ns0="http://sap.com/xi/XI/System">
<Item>
<Operation>Delete</Operation>
<GroupID>0ec543a0bb2311dbceb90016e6905679</GroupID>
<Context>http://sap.com/xi/XI</Context>
<Identifier scheme="Source1" agency="Source">4100058403</Identifier>
</Item>
<Item>
<Operation> Delete </Operation>
<GroupID>0ec543a0bb2311dbceb90016e6905679</GroupID>
<Context>http://sap.com/xi/XI</Context>
<Identifier scheme="Target1" agency="Target">rcjv</Identifier>
</Item>
<Item>
<Operation>Insert</Operation>
<GroupID>0ec543a0bb2311dbceb90016e6905679</GroupID>
<Context>http://sap.com/xi/XI</Context>
<Identifier scheme="Source1" agency="Source">4100058404</Identifier>
</Item>
<Item>
<Operation> Insert </Operation>
<GroupID>0ec543a0bb2311dbceb90016e6905679</GroupID>
<Context>http://sap.com/xi/XI</Context>
<Identifier scheme="Target1" agency="Target">rcjv1</Identifier>
</Item>
</ns0:ValueMappingReplication>
Check Appendix section:
Thanks
Amit Srivastava