Debian 9 update breaks PHP

The best idea is to never install mod_php.

And, if you have installed mod_php, the best thing you can do is uninstall it. Virtualmin will have put in mod_php directives for all of your sites to disable mod_php for those sites, though, so you’ll need to clean that up (mod_php is very disruptive, breaking all other execution modes in a variety of ways if it is not accommodated in the Apache config).