Unless the plugin is in the WP Plugin repository, WP will not ‘see’ the latest version of the update.
Other than putting the plugin in the repository, you will have to manually update your plugin via FTP. Assuming that you are the author of the plugin, you should know when the plugin has a new update, so FTP it to the site.
Even if your plugin is in the WP Plugin repository, you would have to manually update it via the Admin Update panel.
Seems to me that you (the plugin author) should just FTP it to the site when you write/release the updated code.
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