Virtualmin (the virtual-server package) updates won’t remove packages.
We did remove the dependency on mod_php from a couple of the lamp stack packages and one of the yum groups, but that would also not remove mod_php unless you also followed it with apt-get autoremove and chose to remove the packages it suggested (if there were no other packages depending on e.g. php).
So: If mod_php was removed, you removed it. But if Virtualmin is not handling mod_php being missing correctly, that’s a bug (maybe a new bug introduced by fixing an old bug). I’m not clear on whether that’s the case.
You should not be running anything with mod_php at this point. It was a bug that php was installed at all by default on some systems. But, if you are running it, you definitely don’t want to uninstall it (using autoremove or whatever mechanism), until after you switch your apps to something else. Virtualmin updates won’t uninstall it automatically, but the change to lamp-stack to remove it as a dependency might have caused some folks to uninstall it accidentally if they follow it up with an autoremove.