Directive 'register_long_arrays' is no longer available in PHP

[MicheleB]

Hello,
I've a problem with a script and the php function "register_long_arrays".

I need to disable/remove it from my 11.5 Plesk installation, but I don't know how to do it.
I asked my hosting provider (I've a cloud server) and they have disabled it from the control panel, in the PHP settings (Additional directives) with these instructions:
register_globals = Off
register_long_arrays = Off
register_argc_argv = Off


I've tried but the script continues to generate this error:
"Directive 'register_long_arrays' is no longer available in PHP"

In the "php info page" I saw two php.ini for that domain where the script is installed:
/etc/php5/apache2/php.ini
/var/www/vhosts/system/{domain}/etc/php.ini

The first is the general php.ini for all the server, the second (I have hidden the real domain for privacy reason) is not available, doesn't exist.

In the general php.ini ("/etc/php5/apache2/php.ini") I've found these instructions:
register_globals = Off
register_long_arrays = On
register_argc_argv = On
auto_globals_jit = On

I've asked to my hosting provider but they said me that isn't necessary modify this php.ini, and is necessarily need to take action only from the control panel (PHP settings > Additional directives).

Should I edit manually the "/etc/php5/apache2/php.ini" or the operation could create unstable server?

Thanks