During Alt-PHP packages update, we don't rewrite *ini files at all. Only two PHP variables are reset to the values from the native php.ini file, they are "error_log" and "date.timezone".
To prevent this situation, you should define "error_log" and "date.timezone" values in /etc/cl.selector/global_php.ini file and run the following command to apply changes:
As a result, all settings from the files above will be taken for *ini files for all versions inside PHP-Selector.
The current incarnation of PHP Selector is that it will not overwrite Alt-PHP ini files if values in them are different from defaults as that could break websites functionality. You have to run a command with a key to overwrite them. Please read more at http://docs.cloudlinux.com/index.html?configuring_global_php_ini_opt.html