Yes if you make changes to your style.css file and manually upgrade then it will be overridden. That’s how WordPress and Genesis works by default. However, you could create a custom css file so that any updates won’t be affected by the style.css file.
Keep in mind, there aren’t that many updates that are made to child themes. Any updates that are made are usually minor updates, and nothing to be concerned about. The Genesis Framework has updates, but they don’t affect child theme customizations.