To manually delete an SSL certificate you need to login as root and then run these commands.
grep -irn 'example.com' /etc/letsencrypt/
find /etc/letsencrypt/ | grep -i example.com
Then you need to delete the directories and one-two conf files.
Before the deletion inspect the output carefully to make sure you're not deleting the data that belongs to anther domain.
As a safety measure you could move the directories & files into root's home directory directory.