The strange part is that deleting the letsencrypt folder removes the missing certificate errors and lets me start over. I have the original backed up. When I try to get a new cert, it seems to work, a bunch of info is displayed and the folder is recreated and certs are added. I restored the backup and no have the "Ooooops: Certificate not found." error on the Lets Encrypt page as well as the missing certificates error on the cert manager page. I ran the grep commands and this is what I get.



Here are the files:


I noticed that the certs have a 1 in the name but the symbolic links do not. Not sure if that could be the issue. I guess it depends on if the apps access the certs via link or directly. Now I have requested certs too many times and have reached the certbot limit. The /etc/pki/CA/sys-0-cert.pem cert is still in place as well.