To add a custom field value to WooCommerce emails use the following snippet.

/* 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;
}

Add this code to your child theme’s functions.php file or via a plugin that allows custom functions to be added, such as the Dessky Snippets plugin. Please don’t add custom code directly to your parent theme’s functions.php file as this will be overwritten completely when you update the theme.