No need to update anything else. Yes, if the user started at https://sportsmedicalcertificates.com, then when they returned from paypal it would go to https://www.sportsmedicalcertificates.com and they would be in a new session, so the cart would be cleared.
It doesn't have anything to do with paypal settings, and not other pages need to be updated since that is the only one that sends people to paypal's site and specifies a return url.
I would add that htaccess file to any site you have paypal express checkout on. Really SEO gurus suggest using one or the other consistently anyway so your site doesn't get treated like two sites by google and decrease the ratings of both since traffic will be divided between the two.