Every now and again, dread, you have a number of configuration files that have an incorrect value. Recently we encountered this problem on an Apache server. It seems CGI PHP execution mode wasn’t present and we need to remove the flag php_admin_value en mass. The command to achieve this is below and can be easily adapted for other strings and files:
sed -i "/\b(php_admin_value)\b/d" /etc/apache2/sites-available/*
Happy hunting.