If custom PHP directives cause problems, return the affected configuration to a known baseline.
Current cPanel documentation notes that deleting a domain's or home directory's custom php.ini file resets PHP INI settings to defaults for that scope. However, cPanel can also write related values into .user.ini and, when supported, .htaccess.
Before deleting or changing configuration files, save a copy. After resetting, reopen MultiPHP INI Editor and test the application to confirm which values are now inherited from the server configuration.