Certbot does not have any HespiaCP integration. Sounds like HespiaCP is in the lead here regarding your nginx/Apache configuration, so my suggestion is to not let Certbot mess up the webserver configuration, but make the changes in HespiaCP yourself.
Note that after issuance/renewal, any service including webservers using the certificate would need to be reloaded. Not sure how that would be done using HespiaCP, but note that Certbot has the --deploy-hook
option to run scripts after a renewal.