@gongomgra, thanks for your input.
I have decided to restore a snapshot instead (changed ip address, then made new keys, etc etc). I think I have ruined my server when I installed and deployed bncert.
Afterwards, I manually renewed the all expired SSL with this command: sudo /opt/bitnami/letsencrypt/lego --tls --email="EMAIL-ADDRESS" --domains="DOMAIN" --path="/opt/bitnami/letsencrypt" renew
All that's left to do is make the cronjob.