1. Drop and run this script in the root wpmu directory:

<?php
define('WP_INSTALLING', true);
require_once('wp-load.php');

$old_domain = 'olddomain.com';
$new_domain = 'newdomain.com';

$query = "UPDATE wp_site SET domain = '$new_domain' where domain = '$old_domain'";
$wpdb->query($query);

$query = "UPDATE wp_blogs SET domain = REPLACE(domain, '$old_domain', '$new_domain')";
$wpdb->query($query);

$querystr ="SHOW TABLES LIKE 'wp_%_options'";

$tables = $wpdb->get_results($querystr, ARRAY_N);

echo count($tables);
$query = "";
if ($tables){
  foreach ($tables as $table){
    $query = 'UPDATE '.$table[0]." SET option_value = REPLACE(option_value,'$old_domain','$new_domain')";
    $wpdb->query($query);
  }
}
?>

2. Edit wp-config.php and set “DOMAIN_CURRENT_SITE” to the appropriate domain.

That’s it, everything should work properly.