letsencrypt-cpanel
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Subdomains Certficates.
trafficstars
Looks like the plugin doesn't look at sub domains. Can't seem to get my sub-domains in the list from Cpanel.
It works for me. Check if you already have ssl certificates for those subdomains, in which case you would need to remove them first to be displayed in the list.
@Robvred can you access the files within .well-known via a url request?