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While doing upgrade from 11g - 12c you must have used pre-upgrade console to upgrade ( out of place upgrade) existing agents to em 12c agent. If you have done the switchover or done with you whole upgrade process , then you figure out why upgraded agent is not working then reinstalling is bad idea especially when its the agent with the OMS. You need to debug the problem with oracle support.
Pre-upgrade console has lot of healthcheck to make sure that the upgraded agent is all ok and ready to work. If you didn’t see any issues with the healthcheck report then something or some one manually played around with the upgraded agent.