Hoping you deleted SSL from CloudFlare as advised here How to get Cloudfare SSL? - #10 by josephgodwinke
You need to remove private keys and certificates at the Virtual Host Level
Go to OLS WebAdmin Console of your server i.e https://SERVER_URL:7080 use admin and password you chose for CyberPanel admin panel
If you cannot log in. Using SSH Terminal run adminPass add new password

Then you delete all private keys and certificates for respective website and hostname from server:
$ rm -f /etc/letsencrypt/live/mydomain.net/privkey.pem && rm -f /etc/letsencrypt/live/mydomain.net/fullchain.pem
$ rm -f /etc/letsencrypt/live/mail.mydomain.net/privkey.pem && rm -f /etc/letsencrypt/live/mail.mydomain.net/fullchain.pem
$ rm -f /etc/letsencrypt/live/ssl.mydomain.net/privkey.pem && rm -f /etc/letsencrypt/live/ssl.mydomain.net/fullchain.pem
Then resissue hostname SSL the CyberPanel way:
- Go to https://server.mydomain.net:8090/manageSSL/sslForHostName
- Choose
mydomain.net - Click on Issue SSL
If its not hostname domain
- Go to https://server.mydomain.net:8090/manageSSL/manageSSL
- Choose
mydomain.net - Click on Issue SSL