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/* To use: 
1. Add this snippet to your theme's functions.php file
2. Change the meta key names in the snippet
3. Create a custom field in the order post - e.g. key = "Tracking Code" value = abcdefg
4. When next updating the status, or during any other event which emails the user, they will see this field in their email
*/
add_filter('woocommerce_email_order_meta_keys', 'my_custom_order_meta_keys');

function my_custom_order_meta_keys( $keys ) {
     $keys[] = 'Tracking Code'; // This will look for a custom field called 'Tracking Code' and add it to emails
     return $keys;
}