AFAIK you'd want to edit the /etc/vfilters/domain.com file to something along the lines of the following. Beware that cPanel may overwrite the custom command if the filters are subsequently edited via the cPanel interface, as it doesn't deal with "does not contain" at this point in time. I'm not sure there's any danger of the file being overwritten under other circumstances, for example a nightly update etc, but I'm about to try this myself.
$message_headers does not contain "Special-String"
save "/dev/null" 660