It’s possible that Virtualmin installed and started php-fpm - but that service wasn’t set to start at boot. Then if you server restarted for some reason - your sites went down.
The standard install - I suspect won’t start everything at boot, when installed.
It’s possible you installed with a certain version of php and php-fpm set to start at boot. Then a later version of php got installed and the newer Virtual Server got set to use that, it’s php-fpm server started but wasn’t set to start at boot.
A subsequent server restart and one site works (probably on an older version of PHP) and the other doesn’t (on a later version of PHP).
It’s a hypothesis.
HIH
Dibs