I just got done debugging my scripts to install certificates for my domain, and decided to move onto my mail server setup.
When I looked into my /etc/letsencrypt/live folder, I noticed two folders there for my domain; one of them appended with -0001.
So I deleted them and tried again, but got an error:
2016-03-03 05:17:15,114:WARNING:letsencrypt.cli:Renewal conf file /etc/letsencrypt/renewal/mydomain.tld-0001.conf is broken. Skipping. 2016-03-03 05:17:15,119:WARNING:letsencrypt.cli:Renewal conf file /etc/letsencrypt/renewal/mydomain.tld.conf is broken. Skipping.
So I went through the other folders and deleted all references to my domain and tried again. But this time I got a different error:
There were too many requests of a given type :: Error creating new cert :: Too many certificates already issued for: mydomain.tld.