If your domain's authoritative nameservers are set to CloudFlare, you just need to add the A record for the panel subdomain pointing to the IP of your control panel server. It will then be possible to issue the Let's Encrypt certificate.
Alternatively you could delegate the panel subdomain to your Enhance cluster DNS servers.
If the DNS is pointing correctly (if you can browse to your control panel domain) check the server's upstream DNS resolver doesn't have the old IP or NXDOMAIN response cached. If it does, you can either wait for the cache to expire or, if you control the resolver, clear its cache manually.
I may have misunderstood the problem. If you can tell us the domain name, we can check the DNS. Feel free to send this in a support ticket if you don't want to post it on the forum.
