Problem with Certificate Auto Renew

Nope, there are two problems with this:

  • It will confuse Certbot, because Certbot will still expect to be able to renew this certificate based on the existence of /etc/letsencrypt/renewal/mysite.com.conf.
  • It will break Apache, because your Apache configuration in default-ssl.conf refers to these files! If you try to start Apache while referring to a file that doesn't exist, Apache will fail to start.

I would suggest changing mysite.com in these paths in default-ssl.conf to mysite.com-0001. Then you can use certbot-auto delete --cert-name mysite.com to remove the old certificate.