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On Plesk for Linux mod_status is disabled on upgrades to improve Apache security. This is a one-time operation that occurs during an upgrade. You can manually enable mod_status later if needed.
I think it is expected behavior. The message that is being displayed and that is warning the user that files will be deleted applies to a domain removal that happens on the subscription level. In that case indeed the directory tree will be removed. But inside a subscription it makes sense that the data remains in a directory and the directory is not removed, because other parts of the same subscription could still need the files.