Removing Subdomains From A Let’s Encrypt Certificate

# Make a backup just in case.
sudo cp -r /etc/letsencrypt /etc/_letsencrypt

# Remove the old certificate information.
sudo rm -r /etc/letsencrypt/archive/domain.tld
sudo rm -r /etc/letsencrypt/live/domain.tld
sudo rm /etc/letsencrypt/renewal/domain.tld.conf

# Generate a new certificate with the subdomains you want.
sudo /opt/letsencrypt/certbot-auto certonly --webroot -w /path/to/my/app -d 'domain.tld,www.domain.tld'

# Reload Nginx.
sudo service nginx reload

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