Yes anytime you customize a child theme’s css and update the css file, then everything will be overwritten. I always recommend saving your customizations at the bottom of your css file and transferring it to the newly updated file whenever there is an update.
You could also add a custom.css file to the theme and link to it from their style.css file which means future updates won’t effect it.
You can also add css code to your Genesis Theme Settings…..but if you do that, I’d recommend saving your css somewhere locally just in case you accidentally reset your settings.