Upgrading an encapsulated plugin
Once you have created an encapsulated plugin, upgrading it is mostly a matter of creating a new version number under the plugin name, and then making your changes.
So if the old plugin was structured like this:
you can rename this to
and make your changes. Once you release, people will upload the new version and run through the upgrade process using Admin > Modules > Plugin Manager.
Note: One constraint is that even if your first version did not use SQL Installer Classes, your update must do so if there are database changes. The plain .sql files in the Installer folder are not run on an upgrade.