Let’s Encrypt SSL fails with 404 error on sub-server website

SYSTEM INFORMATION
OS type and version any
Virtualmin version any

users @rtyuab @ChenExclus and @Vipul.K reported the same error here here and here

Event when the website was correctly configured, the acme challenge correctly copied in the right public_html/.well-known/ directory, the website perfectly available from outside, Let’s encrypt was returning 404.

I had the same issue and this was an IPv6 problem. For some reason, the website configuration was only defined with the IPv4 address of the server <VirtualHost 192.0.2.196:80> .

Adding back the IPv6 <VirtualHost 192.0.2.196:80 [2001:db8::8a2e:370:7334]:80> (same for the 443 port) solved the issue.

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