MODULENAME.module

<?php

/**
 * Implements hook_menu().
 */
function MODULENAME_menu() {
  $items['node/%node/edit-line-item/%commerce_line_item'] = array(
    'title' => 'Edit line item in the cart',
    'page callback' => 'node_page_view',
    'page arguments' => array(1),
    'access callback' => 'MODULE_edit_line_item_edit_access',
    'access arguments' => array(1, 3, 'access checkout'),
  );
  return $items;
}

/**
 * Implements hook_views_data_alter().
 *
 * Overrides cart_line_item_link_edit handler.
 */
function MODULENAME_views_data_alter(&$data) {
  $data['commerce_line_item']['cart_line_item_link_edit']['field']['handler'] = 'MODULENAME_handler_field_cart_line_item_link_edit';
}

/**
 * Access callback for node/%node/edit-line-item/%commerce_line_item.
 */
function MODULENAME_edit_line_item_edit_access($node, $line_item, $permission) {
  $context = $line_item->data['context'];
  if (($context['entity']['entity_type'] != 'node') || ($context['entity']['entity_id'] != $node->nid)) {
    return false;
  }
  return commerce_cart_line_item_form_menu_item_access($line_item, $permission);
}

/**
 * Implements hook_module_implements_alter().
 *
 * Invoke our hook_field_attach_view_alter() before commerce_cart's one.
 */
function MODULENAME_module_implements_alter(&$implementations, $hook) {
  if ($hook == 'field_attach_view_alter') {
    $key = 'MODULENAME';
    $group = $implementations[$key];
    unset($implementations[$key]);
    $implementations = array($key => $group) + $implementations;
  }
}

/**
 * Implements hook_field_attach_view_alter().
 *
 * Replace the line item argument to the add to cart form with the one being edited.
 *
 * @see commerce_cart_field_attach_view_alter().
 * @see MODULENAME_module_implements_alter().
 */
function MODULENAME_field_attach_view_alter(&$output, $context) {
  if (arg(2) == 'edit-line-item') {
    $line_item = menu_get_object('commerce_line_item', 3);
    if ($line_item) {
      $output[DISCOVER_PLAN_FIELD_PRODUCT_REFERENCE][0]['#arguments']['line_item'] = $line_item;
    }
  }
}

MODULENAME_handler_field_cart_line_item_link_edit.inc

<?php

/**
 * Field handler to present an edit link to a cart line item.
 */
class MODULENAME_handler_field_cart_line_item_link_edit extends commerce_cart_handler_field_cart_line_item_link_edit {
  function render($values) {
    $text = !empty($this->options['text']) ? $this->options['text'] : t('edit');
    $line_item_id = $this->get_value($values, 'line_item_id');

    $line_item = entity_load_single('commerce_line_item', $line_item_id);
    $display_path = $line_item->data['context']['display_path'];

    $path = $display_path . '/edit-line-item/' . $line_item_id;
    $menu_item = menu_get_item($path);

    // Exit if no access to the menu path
    if (empty($menu_item['access'])) {
      return;
    }

    // Build query parameters
    $query_params = drupal_get_destination();
    $query_params['show_quantity'] = $this->options['show_quantity'];
    $query_params['token'] = drupal_get_token('commerce_line_item_edit:' . $line_item_id);

    // render link
    return l($text, $path, array('query' => $query_params));
  }
}