It seems now you've issued a certificate just for the www subdomain:
While it's perfectly possible to have a single certificate for the apex domain beehaw.org and have another certificate with just the www subdomain for www.beehaw.org, this is not necessary. In fact, it's doubling the amount of certificates issued. Think about when everybody would do that! Then Let's Encrypt would possibly have to issue a million certificates per day more, compared to the 2,5 million certs it issues daily!
@9peppe perfectly explained to you to run certbot with two hostnames as option, so I don't really understand why you went for just the single hostname for a new certificate so you ended up with two certs...
I fail to see the relationship between a custom nginx.conf and having two hostnames in a single certificate. You can use that single certificate at separate points in your nginx.conf if necessary.
If you previously also used the --nginx plugin, that probably should work, yes. Always a good idea to backup your nginx configuration files first before letting a software application modify it.
The --nginx plugin should be smart enough to recognise the places the certificate should be used. Although you say the configuration is custom, so YMMV. At least worth a try I believe. Having just a single certificate makes so much more sense
Error while running nginx -c /etc/nginx/nginx.conf -t.
nginx: [emerg] unknown directive "if($host" in /etc/nginx/sites-enabled/lemmy.conf:27
nginx: configuration file /etc/nginx/nginx.conf test failed
The nginx plugin is not working; there may be problems with your existing configuration.
The error was: MisconfigurationError('Error while running nginx -c /etc/nginx/nginx.conf -t.\n\nnginx: [emerg] unknown directive "if($host" in /etc/nginx/sites-enabled/lemmy.conf:27\nnginx: configuration file /etc/nginx/nginx.conf test failed\n')