WordPress 2.5 comes with a cool feature that lets you automatically upgrade plugins from the admin panel via FTP. This is very handy for most people, but there’s a problem with it. If you’ve done any customization in the “templates” folder, all of your changes will be lost. Forever.
Be sure to backup all of your customizations before you upgrade your plugin from the WordPress plugins admin page. If you’re uploading the new files yourself, or upgrading via SVN, you shouldn’t have any problems.