Renewals get all their information from etc/renewal/domain.conf
Review that file as it may explain why you are getting errors
You can review the manual (https://certbot.eff.org/docs/using.html) especially the --allow-subset-of-names flag which should assist in resolving your issues
For now what I’ve done is “ln -s /www/aegis/.well-known /www/complete/.well-known” to get past this month’s renewals. I cannot recreate the SNI problem myself, so it seems the only client going to the wrong page is the certbot auth system. As it received the challenge from the wrong domain in an SNI environment, presumably this is a concern for yourselves?
A) You are using the webroot plugin which is a HTTP Challenge
B) SNI should not play any part in it as it’s a HTTPS (SSL) construct
C) If you are redirecting to HTTP to HTTPS in your server configs it could explain why you are having issues
D) The important test is not to go via HTTPS version of your website but rather via HTTP and observe the behavior from there
All of those websites support both IPv4 and IPv6. I haven’t checked the others, but for https://www.alarmcomplete.co.uk/, IPv4 redirects to one website, and IPv6 has an incorrect certificate and redirects to a different website.
Sorting out the IPv6 configuration issues may solve whatever is wrong here.