Ok i done the troubleshooting from my own.
What i did is uninstall agent on the second machine whose db is not discovered and reinstall the agent back.
Now the problem is sorted out.
But now the problem again arises. I am able to get the status of standby database on OEM grid control. But when i try to perform change of data protection mode, i am getting error that Database standby is not discovered. This problem arise from em grid control only.
Please advice over the same.