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We currently have a dedicated server with one company that is running apache, php, mysql etc. It currently has whm/cpanel installed. We are migrating to a new server with cpanel/whm. Everything migrated over fine but now one of my sites has some php_flag and php_value lines in the .htaccess file. When I go to the site on this new server I am getting 500 errors that read Invalid command 'php_flag', perhaps misspelled or defined by a module not included in the server configuration.

I am not sure what I need to do to get these to work so any help would be greatly appreciated.

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Putting php_flag etc in .htaccess is only possible when you are using mod_php. With CGI/FCGI, Apache settings cannot be used to configure PHP since it is not running within Apache.

Using CGI, if you need a site with a custom php.ini, the exact details would depend on how exactly you're running the PHP (CGI, mod_fastcgi (with or without php-fpm), mod_fcgid). For basic CGI you will need to create an alternate Action for php files in that site that executes a wrapper script containing something like /usr/bin/php5-cgi -c /some/alternate/php.ini

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