So, NodeBB uses .less files to maintain the theming for the site, which then is compiled into .css. The public/css/theme.css file is the compilation of the .less files located in node_modules/nodebb-theme-* You will need to edit the .less files instead of directly editing that css file.
Below are all of the files that should be edited to change the theme.
Screen Shot 2014-02-17 at 3.15.05 PM.png
For more information on LESS. http://lesscss.org/
I hope this helps!