Example of merging commerce orders/carts with hook_commerce_cart_order_convert()

hook_commerce_cart_order_convert_test.php

<?php

// Thanks to http://jasonrichardsmith.org/blog/drupal-commerce-merge-anonymous-carts-when-logging
// for the code on which this is based!

function yourmodule_commerce_cart_order_convert($anon_cart, $account) {

  $user_cart = commerce_cart_order_load($account->uid);

  if (!$user_cart) {
    return;
  }

  $user_cart = entity_metadata_wrapper('commerce_order', $user_cart);

  // Loop through anonymous cart line items.
  foreach ($anon_cart->commerce_line_items as $line_item) {
    // Create an exists flag, which will prevent the whole line item
    // being copied across if it can merge the quantity fields instead.
    $exists = FALSE;
    // Loop through our old, logged-in cart line items.
    foreach ($user_cart->commerce_line_items as $user_line_item) {
      // If the a product in our old cart also exists in the new one,
      // add their quantities together on the user cart and save the line item.
      if ($line_item->commerce_product->product_id->value() === $user_line_item->commerce_product->product_id->value()) {
        $user_line_item->quantity->set((float) $user_line_item->quantity->value() + (float) $line_item->quantity->value());
        $user_line_item->save();
        $exists = TRUE;
      }
    }
    // Assuming that the product hasn't already been added, copy
    // the entire line item over as it is. This is done by setting
    // the line item's order_id to the user cart's id first, then adding
    // it explicitly to the cart, and saving both line item and cart.
    if (!$exists) {
      $line_item->order_id = $user_cart->order_id->value();
      $line_item->save();
      $user_cart->commerce_line_items[] = $line_item;
    }
  }

  // Save our old user cart with new/improved line items/products.
  $user_cart->save();

  // Can't delete the anon cart, because it's required for the
  // next part of the conversion process, and if it doesn't exist
  // then entity.inc will scream at you. Best to cancel and then
  // remove with cron if desired.
  $anon_cart->status->set('canceled');

}