have a look at acme.sh
it doesn’t use links to certs. you define the path to cert files. example from here:
acme.sh --install-cert -d example.com \
--cert-file /path/to/certfile/in/apache/cert.pem \
--key-file /path/to/keyfile/in/apache/key.pem \
--fullchain-file /path/to/fullchain/certfile/apache/fullchain.pem \
--reloadcmd "service apache2 force-reload; service coturn force-reload"
just a tipp. not the solution to your certbot problem.