node_save is not same as saving a node manually
Try one of this options:

Explicit field deletion:

$node = node_load($nid, NULL, FALSE); // Force to load
if (!empty($node-&gt;nid)) {
  $node-&gt;field_taxonomy_term = NULL; // Reset the field
  node_save($node);
}


Submit the node form programmatically:

$node = node_load($nid, NULL, FALSE); // Force to load
if (!empty($node-&gt;nid)) {
  $form_state['node'] = $node;
  $form_state['values']['op'] = t('Save');
  drupal_form_submit($node-&gt;type . '_node_form', $form_state, $node);
}


Edit all nodes on bulk with views bulk operations: 


Install https://drupal.org/project/views_bulk_operations
Add a new view page of content (node) and set fields as display.
Add field "Bulk operations: Content"
Configure the fields: SELECTED BULK OPERATIONS: "Save content" (check)
Save the view and go to the views path.
Select all items and the "Save" operation and execute it!
Done!