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 write your custom CSS code inside the file customizables/theme.css and enable it from the control panel under Interface → Branding, see the Color theme section.

You can also 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.