I have 2 subsites on the same apache server both pointing to the same craft database. The original subsite has the normal links, but, the subsite copy has index.php in all of the links. Can someone point me in the right direction to remove the index.php references? NOTE: .htaccess is correct and the same on both sites.
You should have the setting
'omitScriptNameInUrls' => true on either both sites, or in the wildcard config.
<?php return [ '*' => [ // ... 'omitScriptNameInUrls' => true, // ... ] ];
You can read more about it here: https://craftcms.com/support/remove-index.php