First, I doubt this is an ee or letsencrypt not working issue... Instead you probably didn't setup the cron job and you can't renew a cert after it expires. You have to create a new and there isn't a clear way to delete the old one in ee or le.
My recommendation is manually delete the certs as rbrich suggestion here.
rm -rf /etc/letsencrypt/live/YOURDOMAIN
rm /etc/letsencrypt/renewal/YOURDOMAIN.conf
Now you can try to use ee options to install a new one...
If that won't work... You need more hands-on control so I would try install and new cert with certbot.
https://certbot.eff.org/all-instructions/
Once that's done don't forget to add the cron job so you don't have same problem again. 