I think this is really a bug in Certbot (Linux snap version), but I'm reporting this here because I have a work-around that users may find useful:
In 2021, I created a multi-domain certificate using dns-rfc2136 renewals. That created a "renewal/example.com.conf" file with the following lines:
authenticator = dns-rfc2136
dns_rfc2136_propagation_seconds = 300
dns_rfc2136_credentials = /etc/letsencrypt/credentials/ddns-rfc2136.ini
The above has worked for four years. Early this year, I created another certificate using dns-cloudflare renewals. That created a "renewal/addon.com.conf" file with the following lines:
authenticator = dns-cloudflare
dns_cloudflare_propagation_seconds = 10
dns_cloudflare_credentials = /etc/letsencrypt/credentials/cloudflare.ini
That worked. Until the renewal for both certificates came due last Sunday. Note that "addon.com.conf" appears before "example.com.conf" in the "renewal/" directory, so the certificates were processed in alphabetical order (I don't know if that is pertinent). "addon.com.conf" renewed properly, but Certbot complained:
"Missing command line flag or config entry for this setting:
Input the path to your RFC 2136 credentials INI file"
Even though it had been able to find it in "renewal/example.com.conf" for four years. So, I copied the "dns_rfc2136_credentials" line to the "cli.ini" file & that fixed that.
Then, the renewal for "example.com.conf" failed with a bunch of "DNS problem: NXDOMAIN looking up TXT for _acme-challenge.domain.com" messages, even though "dig" clearly showed that the pertinent lines were in the DNS during the process.
Then I noticed the processing message "Waiting 60 seconds for DNS changes to propagate". I copied the "dns_rfc2136_propagation_seconds = 300" line from "renewal/example.com.conf" to "cli.ini" & that fixed that.
Apparently Certbot is not processing the configuration files for multiple certificates correctly. I suspect that if "addon.com.conf" has sorted after "example.com.conf", I would have had to copy its pertinent configuration options to "cli.ini" as well.
You have been warned!