I have both Drupal and WHMCS installed on the same domain, Drupal is the main website and WHMCS is the client portal.
URL’s for file downloads in WHMCS do not work properly because they are being served by Drupal (i.e. Drupal thinks its supposed to be handling the URL and returns an internal Drupal page not found message when clicking on the link), WHMCS itself should be handling the URL.
I think this is simple .htaccess configuration issue and should be very easy to fix for someone with any experience.