Move taxonomy from node to content taxonomy fields. Use with drush.

update_nodes.php

<?php
/**
 * @file
 * Move taxonomy term from taxonomy_node table to field tables.
 */

$types = array(
  array(
    'type' => 'product',
    'fields' => array(
      'field_product_keyword' => 3,
      'field_product_company' => 11,
    ),
  ),
);

foreach ($types as $type) {
  update_nodes($type);
}

function update_nodes($info) {
  $count = 0;
  $vids = array_values($info['fields']);
  $result = db_query("SELECT nid FROM {node} WHERE type = '%s'", $info['type']);
  while ($row = db_fetch_object($result)) {
    $node = node_load($row->nid);
    $tids = array();
    $update = FALSE;

    foreach ($node->taxonomy as $delta => $term) {
      if (in_array($term->vid, $vids)) {
        $tids[$term->vid][] = array('value' => $term->tid);
        $node->taxonomy[$delta] = NULL;
        $update = TRUE;
      }
    }

    foreach ($info['fields'] as $field_name => $vid) {
      if (!empty($tids[$vid])) {
        $node->$field_name = $tids[$vid];
      }
    }

    if ($update) {
      node_save($node);
      $count++;
    }
  }

  printf("%d '%s' nodes have been updated.\n", $count, $info['type']);
}