You probably want to take a look at https://dev.xwiki.org/xwiki/bin/view/Onboarding/TrackStyling/
You can add native CSS or LESS using StyleSheet Extension objects on one of your page.
I don’t advise you to change files in your distribution’s folder directly. You could break something easily.
AFAIK the style.css file is generated from various sources, my guess is that your changes are deleted on every new generation of the file.
Have a good day,
Lucas C.