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Before you delete the folders, make sure to go into your cPanel to "Frontpage Extensions" and make sure they are not installed for your main domain or any subdomains.
This is also a strange side-effect:
Installing or uninstalling FrontPage Extensions will result in the loss of all .htaccess files in your web area. Any directories you have protected with WebProtect will become unprotected until you reprotect them.
So you will need to backup your .htaccess file and upload again, and take note of what you have used with WebProtect. I have personally not tested this myself, and it may not even remove the settings on protected directories..
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