I think it will wait for a while, but it could be very confusing if you reload php-fpm without taking the web server into account. I stop apache first, then stop php-fpm, then start in reverse order. Application design makes a difference; php makes sense for requests that run quickly and then finish, but some applications have long running php scripts that can cause all kinds of problems, e.g. phpmyadmin has a script to import a database that can run for ages.
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