I am trying to remove the default lightbox.js file coming from the Lightbox2 module, by using template.php, and load in my own. I would like to do this via template.php if possible, and not place this code in a custom module. I am adding my javascript file, then unsetting the module javascript file. The problem is $vars['scripts'] isn't getting replaced with the output from $js, and still outputting the module javascript. krumo($js) shows the default lightbox.js removed. Below is what I have in template_preprocess_page. Thanks in advance.
drupal_add_js(path_to_theme() . "/resources/js/lightbox.js", 'theme');
$js = drupal_add_js(NULL, NULL, 'header'); //get header js files in an array
$lightbox_path = drupal_get_path('module', 'lightbox2');
unset($js['module'][$lightbox_path . '/js/lightbox.js']); //unset lightbox default js
$vars['scripts'] = drupal_get_js('header', $js);