In the File Manager all domains/subdomains have their own folder. After deleting one of the websites from the control panel their directory remains. When I try to delete the folders manually I get an error. How do I delete the folders?
You cannot delete those folders. They will not affect your site.
Since those folders are stored outside of the website root, you do not have permission to edit them. Instead, you can rename them to something like [deleted] if you wish.
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