Override a file from the parent theme
You can use hook_js_alter to replace your JS file (from parent theme) with the one in your child theme.
function child_theme_name_doc_js_alter(&amp;$javascript) {
  $javascript['themes/parent_theme_name/js/parent_theme_name_navigation.js']['data'] = drupal_get_path('theme', 'child_theme_name') . '/js/child_theme_name_navigation.js';
}