Automatic update of existing nodes

May I ask why you want to do that? You need to run the update only once, when the module is installed. Afterwards the corresponding node references are created without running the update.

OK, I see. This is not a very common use case... Anyway, putting this in any module worked for me:

<?php
function MYMODULENAME_cron(){

  $options = node_get_types('names');
  foreach ($options as $type => $name) {
    $options[$type] = $type;
  }

  $form_state = array();
  $form_state['values'] = array();
  $form_state['values']['types'] = $options;
  drupal_execute('corresponding_node_references_update_form',$form_state);

}

Just for the record, for D7 it looks like this:

<?php
function MYMODULENAME_cron(){
  $options = _node_types_build()->types;
  foreach ($options as $type => $class) {
    $options[$type] = $type;
  }

  $form_state = array();
  $form_state['values'] = array();
  $form_state['values']['types'] = $options;
  drupal_form_submit('corresponding_node_references_update_form',$form_state);

}

Hope it helps.

I forgot to say (just in case it wasn't clear): this code updates corresponding node references every time cron runs. (Which might be quite resource consuming.)

No new features will be added. New features can be posted on http://drupal.org/project/cer which is the next evolution of cnr.