I still don't fully understand the question.
If you had URLs that looked like
www.example.com/index.php/this-page and you now have URLs that look like
www.example.com/this-page you do need to add a redirect so that when the old URL is requested, the user is redirected to the new one.
RewriteRule ^index\.php/(.+) http://www.example.com/$1 [R=301,L]