Thanks for the link, I tried
cd /var/lib/letsencrypt && sudo ./renew-certs.py
And get…
Certificate file /etc/nginx/ssl/letsencrypt/domain1.cert already exists
The certificate is younger than 60 days. Not creating a new certificate.
So something must be up with the configuration just not recognising the other two domains and creating certificates for them.
Which is odd because I was having issues with the DNS yesterday where it was asking to double check that correct A Records all existed – and they do now – so some part of the server provisioning understands that there’s three domains but something else doesn’t recognise them.