theme-woocommerce.php

<?php

/*
* When using the 'pay for order' link with a WooCommerce Subscriptions renewal order, WCS recreates the order in the cart (setup_cart() in class-wcs-cart-renewal.php)
* However it does not copy custom order item meta to the cart items as cart item meta. This has to be done with the filter woocommerce_order_again_cart_item_data
*/

  function my_custom_add_renewal_cart_item_data($cart_item_data, $line_item, $subscription){
    //there will be only one set of cart item data, WCS just packages it as an array for this filter
    $cart_item_data = array_shift($cart_item_data);
    if(!empty($cart_item_data['custom_line_item_meta'])){
          foreach($cart_item_data['custom_line_item_meta'] as $meta_key => $meta_value){
              $cart_item_data[$meta_key] = $meta_value;
          }
    }
    return $cart_item_data;      
  }
  add_filter('woocommerce_order_again_cart_item_data','my_custom_add_renewal_cart_item_data',10,3);