When upgrading a monitored MySQL server, first stop the agent, as explained in:
Stop the MySQL server, then perform the upgrade.
To stop and restart the MySQL daemon under Unix, Linux, and Mac OS X, see, Section 3.2.5, “Starting/Stopping the MySQL Enterprise Monitor Service on Unix and Mac OS X”.
For instructions on stopping and restarting the MySQL service under Windows, see Section 3.2.6, “Starting/Stopping the MySQL Enterprise Monitor Service on Windows”.
Once the service/daemon is stopped, upgrade your MySQL server, using the instructions from the reference manual the new server version. When the upgrade is complete, restart the MySQL server.
The agent's log file shows that the server was down during the upgrade process.