Thread:Project:Support desk/CSS missing from page after removing index.php from url/reply

I guess that you currently can no longer access CSS styles, which are delivered by the load.php file. If this is your problem, then you should add an exception for this file to .htaccess so that calls to load.php are not redirected to MediaWiki, but that they are just left they way they are.

See Manual:load.php and Short URLs for a complete guide!