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I understand that, apparently I was unclear in my post. When the 12c agent was running properly, using the 10g emctl reported that agent was running but not ready. What I learned from Oracle is -
After agent is upgraded to 12C and switch over is done and in the process the old 10G was been stopped automatically.
When issuing emctl command from 10G home its actually trying to contact 12C agent using the emctl from 10G home and the confusion arises here.
There is apparently a bug which will be registered, Bug 16362122 - EMCTL SHOWS 10G AGENT IS RUNNING AFTER UPGRADE TO 12C AGENT.