You should not delete your cgi-bin folder. You'll need them to process your PHP files.
I'm not sure how to get your cgi-bin folder back. Maybe you can try to go to DH panel --> Domains --> Manage Domains --> Web Hosting --> Edit. Disable fastcgi, save change, enable fastcgi, and save changes again.
sXi is trying to help you to clean windows characters in your .htaccess file. Follow his instruction to run dos2unix .htaccess first.
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