As software updates are replacing FileRun's files regardless of the fact that they have been customized, there is a way to make CSS modification which will be preserved between software updates. You can specify the URL of an external CSS file which will get loaded. Simply add the following line inside the configuration file (customizables/config.php):

$config['app']['ui']['custom_css_url'] = 'http://www.your-site.com/your-file.css';

Replace the example URL with your own valid URL.