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"Add On" Domains being referenced as a subdomain

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"Add On" Domains being referenced as a subdomain
My web host allows me to create "Add On" domains. I can host multiple sites with the same account. When doing this it adds an entry to httpd.conf that points my new domain (a different website) to a subdomain of the main website.


ex) newdomain.com points to subdomain.mainwebsite.com


It also creates a folder in the root directory (of the main website) that becomes the root directory of my new domain. I've added another .htaccess file here.

I'm running some .pl scripts (I bought these and can't edit them) in the cgi-bin of the new subfolder. Where I run into problems is that these scripts reference URLs of the new domain as:

subdomain.mainwebsite.com/files not newdomain.com/files

Is this a setting on my host’s server that is causing this?
Or can I use .htaccess to rewrite the subdomain reference with my new domain?