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      // First attempt to delete references to each line item, building a list

      // of modified entities to be saved once each after references to all line

      // items have been deleted.

      $reference_fields = commerce_info_fields('commerce_line_item_reference');

      $modified_entities = array();

        // Check the data in every line item reference field.

        foreach ($reference_fields as $field_name => $field) {

          // Query for any entity referencing the deleted line item in this field.

          $query = new EntityFieldQuery();

          $query->fieldCondition($field_name, 'line_item_id', $line_item->line_item_id, '=');

          $result = $query->execute();

          // If no results were returned, continue to next field.

          if (empty($result)) {

            continue;

          }

          // Loop over results for each type of entity returned.

          foreach ($result as $entity_type => $data) {

            // Load the entities of the current type.

            $entities = entity_load($entity_type, array_keys($data));

            // Loop over each entity and remove the reference to the deleted line item.

            foreach ($entities as $entity_id => $entity) {

              // If we have this entity already, get the reference, otherwise

              // store the new entity to save changes later.

              if (!isset($modified_entities[$entity_type . ':' . $entity_id])) {

                $modified_entities[$entity_type . ':' . $entity_id] = array(

                  'entity_type' => $entity_type,

                  'entity' => $entity,

                );

              }

              commerce_entity_reference_delete($entity, $field_name, 'line_item_id', $line_item->line_item_id);

            }

          }

        }

      }

      // Save the entities that were modified through deleted references.

      foreach ($modified_entities as $entity_data) {

        entity_save($entity_data['entity_type'], $entity_data['entity']);