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when you are doing re-install of 12c OMS and pointing your existing 12c agents to it, it is equivalent of re-pointing 12c agents to other 12c oms.
we can not point 12c agent to different OMS then the one it was originally pointed to. this is documented in MoS note 1390717.1. you need to re-install your 12c agents
I was actually able to reconnect all of my agents without doing a re-installation.
I followed these steps and had no issues:
1. Promote the host agent through the Non-Host Targets under the Auto Discovery Results
2. Shutdown the agent (./emctl stop agent)
3. Secure the agent (./emctl secure agent)
4. Start the agent (./emctl start agent)
5. Ping the OMS to make sure it is connected (./emctl pingOMS)
6. Re-associate the agent (./emctl config agent addcentralagent)
7. Check the Hosts target section and the host I was readding was now showing up with a pending status
8. Go to the Agents setup screen, click on the agent
9. Click on the drop down once in the Agent Status screen and click on Resyncronization
10. After the job completed everything was fine, just promote the targets that are to be monitored