Wordpress multi-site domains pointing to a non-wordpress directory

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When I access my some of the non primary domains hosted from my wordpress multi-site it what shows up instead are the contents of another folder which contains the file for another site that is not hosted through wordpress. The configuration that worked for several years has not changed and I even tried restoring wordpress from a known good backup, but the problem persists.
Hello hbrandes,

Sorry to hear you are having issues with some of your sites not pointing correctly using WordPress multisite. We do need more information in order to attempt to assist. You have a large number of domains on your site, so we need to begin by knowing which domains you are having issues with. Also, have you checked with the WordPress community forums for multi-site? They can also be very helpful in specific issues.

Kindest Regards,
Scott M