Some resources of my website are pointing to www.mysite.com/dev/ and trying to get rid of that append has been a headache

It seems that your software for finding URLs in the database does not find any matches, it might be worth double-checking it with some other method, please see my reply here Wrong domain in uploads folder for more details.

If the CSS file is one of your theme CSS files then most likely the CSS file URL is not stored in the database at all. I would advise checking your theme functions.php or header.php files, my guess is that either the CSS file URL is registered there (using wp_register_style()) function with the /dev/ path or loaded directly in the header.php.