I managed to break the operation of any new sites created on the server by creating a site (and adding SSL) with the same domain that was being used for phpMyAdmin (with SSL). (A silly thing to do in hindsight!)
Deleting the site didn't solve the issue and required manual intervention to remove FPM pool files to allow NGINX to reload with any new changes.
May be worth adding a check against the phpMyAdmin domain when creating a new site to avoid other users breaking their servers?
Hi Dennis, I believe it was the other way around. I created a site on the server which used the same hostname as the existing phpMyAdmin install. I think it was something to do with SSL which then stopped NGINX from being able to restart.