I happen to have neglected my certificates and now they are rotting away. Some have expired, others are pointing to the wrong domain.

First of all, how to get rid of unwanted certificates? we just call

letsencrypt delete

the program will ask which certificate to delete.

We can check that everything is in order with

letsencrypt certificates

Then we set up the new certificate with

letsencrypt

which will parse the apache configuration and suggest what to do.