Updating the plugin is very easy. When an update is available for Pretty Links, WordPress will notify you in your dashboard. Simply click on Plugins, and scroll down to Pretty Links and Click “Update Now”.
If Automatic Updates do not work on your site, then please follow the Manual Installation instructions, but before installing the latest version — Deactivate and Delete the old version of the plugin. Don’t worry, doing this will not delete your saved data, or links.