Enable media module and process all the files in 1 step.

my_module.install

<?php

/*
  If you have a large number of existing files then you will want
  to implement batch in hook_update_N(). I didn't need that so it
  isn't implemented here. If you need it read this article
  http://bleen.net/blog/running-batch-processes-update-hook-bed
*/

/**
 * Implements hook_update_N()
 */
function my_module_update_7123() {
  $modules = array(
    'media',
    // any other modules
  );
  module_enable($modules);

  // Replicates media_admin_rebuild_types_batch_op() without the batch
  while($remaining = media_type_invalid_files_count()) {
    media_type_batch_update(FALSE, 100);
  }
  
  // Remove nag as per media_admin_rebuild_types_batch_complete().
  media_variable_del('show_file_type_rebuild_nag');
}