How can I remove Javascript files?
This how solved my problem.

Found out that jquery_update uses hook_theme_registry_alter() to unset jquery in Drupal core and replace a new version of Jquery. So this preprocess function is being load after everything all. What I did is I created a hook_theme_registry_alter() and update the weight of the module higher than jquery_update module so I can override the jquery_update_theme_registry_alter(). 

This jquery_update_theme_registry_alter() prevents any alteration in javascript which a big headache if you're working on some adjustments like in my case.

Code:

function my_module_theme_registry_alter(&amp;$theme_registry) {
    global $theme;

    // Only apply this code in mobile theme
    if($theme == 'myTheme') {
    //Attach the my_module_preprocess_page in the theme registry preprocess functions
      $theme_registry['page']['preprocess functions'][] = 'my_module_preprocess_page';
    }
}

function my_module_preprocess_page(&amp;$variables) {

    // Perform the logic if either jQuery Update's jquery.js is newer than core's.
    if (variable_get('jquery_update_replace', TRUE)) {
        // Get an array of all the JavaScript files loaded by Drupal on this page.
        $scripts = drupal_add_js();

        // Replace jquery.js first.
        $new_jquery = array(jquery_update_jquery_path() =&gt; $scripts['core']['misc/jquery.js']);
        $scripts['core'] = array_merge($new_jquery, $scripts['core']);
        unset($scripts['core']['misc/jquery.js']);

        // Loop through each of the required replacements.
        foreach (jquery_update_get_replacements() as $type =&gt; $replacements) {
            foreach ($replacements as $find =&gt; $replace) {
                // If the file to replace is loaded on this page...
                if (isset($scripts[$type][$find])) {
                    // Create a new entry for the replacement file, and unset the original one.
                    $replace = JQUERY_UPDATE_REPLACE_PATH .'/'. $replace;
                    $scripts[$type][$replace] = $scripts[$type][$find];
                    unset($scripts[$type][$find]);
                }
            }
        }
        // Unset javascripts that is/are not needed in mobile theme
        unset($scripts['module']['sites/all/modules/boxes/boxes.js']);

            .....

        // Recreate the scripts variable
        $variables['scripts'] = drupal_get_js('header', $scripts);
    }
}


Hope this will help others. Please let me know if this approach is a violation. Thanks