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I'm not sure that changes to the global php.ini file (/etc/php.ini) are persistent. AFAIK, Plesk overwrites the /etc/php.ini file each time Apache restarts/reloads.
In Plesk 11.x...
Changes that are specific to a particular service plan should be made in Service Plans -> Your Plan -> PHP Settings: Additional Directives
Changes that are specific to a particular subscription should be made in Subscriptions -> Your Domain -> Customize -> PHP Settings: Additional Directives.
Main php.ini that is being used if the one at .../domain.ltd/etc/php.ini is missing is at /etc/php5/cgi/php.ini.
Also, if i change some settings at "/usr/share/php5/php.ini-production", that is being replicated on every newly created domain.
I'm thinking of making cron which will erase all default php.ini-s under domain.ltd/etc/php.ini so that my clients dont' override core php.ini.
p.s. I REALLY DON'T UNDERSTAND HOW IS THIS POSSIBLE. Some in Parallels decided to do this leaving users without any article about it and forcing them not to be able to have global php.ini excempt maybe through some web interface...which you can never know what is being done...
I believe that clients' ability to modify the subscription's php.ini can be disabled. Read the article "Customize PHP Configuration" in the Administration Guide for more information.