Solution: Switching to rewrite rules
Redirect old url conventions/patterns
If you're switching from a setup where index.php is occuring in the URL, to a rewrite rule based setup, you can make sure any old links are properly redirected (with HTTP status MOVED PERMANENTLY) to the new URL without index.php. Put this in the appropriate virtual host context of your Apache configuration:
RewriteRule ^/index\.php/(.*)$ /$1 [L,R=301]