Thanks @anahata for the info to edit apache2/sites-available/*.
In case it’s not obvious, you change the SetHandler line (both of them if you it’s an SSL site) to have a port number that matches the “listen =” line in the PHP conf file. You then have to restart both services apache2 and php7.0-fpm.
is there an ETA for an official fix?
I’m running virtualmin (LEMP installation) on Ubuntu 18.04.3 LTS and can confirm that running “Re-Check Configuration” messes up my nginx + php-fpm port settings every time. The nginx conf files retain the original port settings, but the numeric conf files in /etc/php/7.2/fpm/pool.d/ are all assigned new numbers which do not correspond with their associated nginx conf files. This results in a 502 server error when accessing the web sites. The solution is to manually edit all the numeric conf sites so that their listen directives have the correct port numbers.
The conf files have this naming convention: [domain-id].conf
It would have been much easier if they had adopted [domain-name].conf instead.
If you’re hosting a lot of domains, you would have to keep an index file of domain-id, domain-name so you can quickly find the correct conf file to edit for a given domain name. Manually editing each conf file to correct the ports that re-check bug creates would become very tedious very soon when dealing with a lot of domains.
This is definitely a high priority fix, because right now, using re-check configuration is BROKEN.
Did someone test / noticed / noted what all changed exactly when not working anymore?
I do every single update and I first noticed the problem on the update prior to the last one (the one to fix the password reset vuln)
Same thing happened to me. Took me a while to figure out the cause, so all sites were offline for like half an hour. 
Welcome in the club…
So yesterday I have changed ports for all nginx virtual hosts to new fpm ports, so I brought all sites back up. Today I have changed some unrelated configurations in webmin / virtualmin which somehow caused port change again, meaning that virtualmin regenerated fpm pool files for all installed PHP versions in:
/etc/php/7.0/fpm/pool.d/
/etc/php/7.1/fpm/pool.d/
/etc/php/7.2/fpm/pool.d/
/etc/php/7.3/fpm/pool.d/
making new port numbers for existing pools bringing all sites offline again.
This is critical bug, which should be addressed as soon as possible.
Meanwhile, what can I do to prevent these port changes in future, is there something I can do to prevent it?
Guys can anyone confirm that in Webmin>Bootup options, php-fpm status is set to “start on boot” (this was the solution on my system for this error… php-fpm somehow was no longer set to start on boot)
In my case it was: start on boot -> activated
Same, Start on boot is activated
has this been fixed yet?
I am still having to change all domains from php-fpm to fcgid and back again every time i either run an apache update or virtualmin>system>recheck configuration
This is incredibly frustrating when trying to problem solve other things…one runs a recheck config and then domain php driven websites all go offline. such a time waster, not happy!!!
UH you write here.?
My install of virtualmin has no longer experienced php fpm issues for a while now.
https://www.virtualmin.com/comment/817827#comment-817827
There are at the moment many many to many open …