Tan solo tenemos que ejecutar en consola:

sudo certbot delete

Y nos devolverá nuestra lista de certificados:

Saving debug log to /var/log/letsencrypt/letsencrypt.log

Which certificate(s) would you like to delete?
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
1: ejemplo.com-0001
2: ejemplodos.com
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
Select the appropriate numbers separated by commas and/or spaces, or leave input
blank to select all options shown (Enter ‘c’ to cancel): 1

Seleccionamos el número que queremos y pulsamos «Enter».

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También podríamos ejecutar directamente:

sudo certbot delete --cert-name ejemplo.com

Y listo!