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If you implemented a custom authentication backend and want to change the username provide by the user after authentication. Then implement your checkPass function with the $user parameter passed by reference:

function checkPass(&$user,$pass)
{
  if(user_authenticated($user,$pass)){
    $user = $some_unique_id_fetched_from_your_own_user_db;
    return true;
  }else{
    return false;
  }
}