Just as a note, if you delete the .conf file without deleting the corresponding live and archive directories, you may encounter problems if you create a completely new certificate whose first domain name is exactly the same as the previous one. (Renewal should be fine.)
(If example.com.conf doesn’t exist anymore but live/example.com and archive/example.com do, no new certificate lineage can be created successfully whose first domain is example.com. Maybe we should have better error handling for this situation.)