Darkle
You could be right, I am sure the folder does not have write permissions, will run the command and retest.
update
I ran the command below, but still no luck, Flarum is located under the HTML directory
sudo chown www-data:www-data -R /var/www/
Fix
In order for it to work again, I ran the command above to give the www folder write permissions, copied the CSS and JS files back into the assets folder, go to admin, make the changes and save, the new CSS file was updated.