Unfortunately, you should have used the “Custom CSS” field, a custom CSS plugin, or a child theme to make your changes. Any changes done directly on the theme files (style.css, js files or php files) are lost after an update. This is default WordPress behaviour and cannot be changed.
Theme settings, including the contents of the “Custom CSS” field, are kept between updates.
The only way to get your customizations back is to grab the files out of a backup. If you do not have a backup, then you’re out of luck. Sorry!