wpdb update multiple row?

Your code of wpdb method is correct.
posible reasons why it fails…

1. you have only one user that match’s meta_key = ‘user_token’
2. other functionality change query at query hook filter strage.

debug the final SQL with

add_filter( 'query', 'query_report', 10000 );
function query_report($sql){ 
    var_dump($sql); 
    return $sql;
}