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In 12c, there are no special settings or steps for deploying agents to a cluster. You simply deploy an agent to every node of the cluster, just like you would on an individual server. Once the agent is deployed, the data collected about these nodes will be used to construct the cluster targets in EM. Unfortunately, any issues with data collections or dynamic properties or associations, etc can cause these clusters or its nodes to show incorrect status, or not be formed as complete targets.
Best to file an SR and have support look at your environment.
In addition to the previous response - I too have experienced issues after switching clustered agents using the 2-System upgrade method. They either end up in pending state, blackout or both. In all cases I had to open an SR to help resolve the issues. There isn't any special configuration required for the agents.
Hope this helps.
Thank you. I have a ew more things to try before I open an SR.