Copy of subsite is still serving index.php in the links?
You should have the setting 'omitScriptNameInUrls' =&gt; true on either both sites, or in the wildcard config. 

&lt;?php

return [
    '*' =&gt; [
        // ...
        'omitScriptNameInUrls' =&gt; true,
        // ...
    ]
];


You can read more about it here:
https://craftcms.com/support/remove-index.php