MSM and .htaccess

Hi, Exploring taking the /index.php/ out of our 4.3.n ‘site; the EE docs’ solution works fine for the primary but not the secondary one in our MSM configuration. It’s not served from a different domain or subdomain, just a directory… like example.com/ and example.com/site-two. Putting the .htaccess file in the root of the secondary didn’t solve the problem, 404s for all content. I’m not a regex hero, so I may be missing something obvious… Open to suggestions, thanks.