With the R2 upgrades, I also upgraded a couple of management servers. The MS method for removing an management server is to first delete the management server object, move the agents and then uninstall the Opsmgr. But deleting the object without first moving all the agents to another management server will get you this error
"The management server is part of the communication topology and cannot be deleted."
and this is because you still have agents and possibly agentless managed objects pointing to that management server. So the correct procedure should be
1. Move all agents to another management server
2. Move all agentless objects to another mangement server
3. Uninstall Opsmgr
4. Delete management server objects from the console Administration/Management Servers right click delete
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