I had r.example.com running with nginx and certbot, then after some time I added base domain example.com and it also worked fine. After that I tried to clear some things so that all configuration should appear in base domain example.com and not in r.example.com (i.e. /etc/letsencrypt/live/r.example.com).
certbot certonly --webroot -w /var/www -d example.com --force-renewal didn’t renew the certificates but created a new configuration with new certificates under /etc/letsencrypt/live/example.com
So what is the correct way to merge those certificates into a single certificate? I also would like to get rid of r.example.com and probably leave only example.com but now I have two sets of certificates and even after reading tons of documenation and topics here didn’t help me a bit. The original intention was to change base domain.