Cloudflare should no longer be issuing Universal SSL certificates using this root. Existing certificates will continue to be used until they expire and are reissued. You can force Cloudflare to reissue the Universal SSL certificate by disabling Universal SSL, waiting a couple of minutes and then re-enabling Universal SSL. Do note that disabling Universal SSL will make your site inaccessible over HTTPS.
If disabling Universal SSL is not an option, please create a support ticket and post the ticket number here. We will make sure it is escalated. Cloudflare Support can then manually reissue the certificate, but it may take a few days.