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MySQL 5.5 Reference Manual
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Excerpts from this Manual Choosing a Maintenance Option

If the MySQL Server Instance Configuration Wizard detects an existing configuration file, you have the option of either reconfiguring your existing server, or removing the server instance by deleting the configuration file and stopping and removing the MySQL service.

To reconfigure an existing server, choose the Re-configure Instance option and click the Next button. Any existing configuration file is not overwritten, but renamed (within the same directory) using a timestamp (Windows) or sequential number (Linux). To remove the existing server instance, choose the Remove Instance option and click the Next button.

If you choose the Remove Instance option, you advance to a confirmation window. Click the Execute button. The MySQL Server Configuration Wizard stops and removes the MySQL service, and then deletes the configuration file. The server installation and its data folder are not removed.

If you choose the Re-configure Instance option, you advance to the Configuration Type dialog where you can choose the type of installation that you wish to configure.