update hook to delete and bulk update pathauto aliases
I do it with the following method:

function MYMODULE_update_7100(&amp;$sandbox) {
  module_load_include('inc', 'pathauto');
  module_load_include('inc', 'pathauto.pathauto');

  // Delete the existing node aliases.
  db_delete('url_alias')
    -&gt;condition('source', 'node/%', 'LIKE')
    -&gt;execute();

  // Regenerate the node aliases.
  $nids = db_query("SELECT nid FROM {node}")-&gt;fetchCol();
  pathauto_node_update_alias_multiple($nids, 'bulkupdate');

  // Delete the topics taxonomy aliases.
  db_delete('url_alias')
    -&gt;condition('source', 'taxonomy/term/%', 'LIKE')
    -&gt;execute();

  // Regenerate the taxonomy aliases.
  $tids = db_query("SELECT tid FROM {taxonomy_term_data}")-&gt;fetchCol();
  pathauto_taxonomy_term_update_alias_multiple($tids, 'bulkupdate');
}