Don’t delete certificates that are actively in use with certbot delete (this command does not have a way of checking whether software on your system is still using those certificates, even if Certbot was originally responsible for configuring the software to do so), and don’t manually delete anything in /etc/letsencrypt. Different versions of Certbot can use the same data in /etc/letsencrypt, so if you uninstall an old version of Certbot and install a newer one, it will continue to understand the information that the previous version put there.
In general, you should only delete a certificate if that certificate was issued in error and is no longer being used at all. If you have a specific problem with your HTTPS site after running Certbot (for example, incorrect redirects or failed validation), you can ask on this forum and people can help debug it—but deleting the certificate is probably not the solution.