When upgrading a monitored MySQL server first stop the agent. To stop the agent see:
Stop the MySQL server and perform the upgrade. For instructions on stopping and restarting the MySQL service under Windows see Section 2.2.5, “Starting/Stopping the MySQL Enterprise Monitor Service on Windows”.
To stop and restart the MySQL daemon under Unix and Mac OS X, see, Section 2.2.6, “Starting/Stopping the MySQL Enterprise Monitor Service on Unix and Mac OS X”.
Once the service/daemon is stopped you may upgrade your server. For instructions on upgrading your MySQL server see the reference manual pertaining to your server version. When the upgrade is complete restart the MySQL server.
The agent's log file will show that the server was down.