maybe this way can slove the 

 KNOWN ISSUE: Any users not available to the UI will be unsubscribed from
 *              content they may subscribe to using some other method.

After send messages, re-subscribe deleted subscribes, unsubscribe added subscribes.

/**
 * Implements hook_action_info().
 */
function druedu_notifications_team_action_info() {
  return array(
    'druedu_notifications_team_resubscribe_action' => array(
      'type' => 'notifications',
      'label' => t('After send messages, re-subscribe deleted subscribes, unsubscribe added subscribes.'),
      'configurable' => FALSE,
      'behavior' => array('sends_notification'),
      'triggers' => array('node_update'),
    ),
  );
}
/**
 * After send messages, re-subscribe deleted subscribes, unsubscribe added subscribes.
 */
function druedu_notifications_team_resubscribe_action($node, $context = array()) {
  if(isset($context['node'])){
    $node = $context['node'];
    $changed_subscribes = $node->notifications_team_all;
    $default_subscribes = druedu_notifications_team_get_subscriptions($node->nid, $reset = FALSE);
    $deleted_subs = array_diff($default_subscribes,$changed_subscribes);
    $added_subs = array_filter(array_diff($changed_subscribes,$default_subscribes));
    foreach ($deleted_subs as $key => $uid) {
      # resubscribe
      // dpm($deleted_subs,'re-subscribe-$deleted_subs');
      $subscription = notifications_subscription('content_thread')
          ->instance()
          ->set_user(user_load($uid))
          ->set_node($node);
      notifications_save_subscription($subscription);
    }

    foreach ($added_subs as $key => $uid) {
      # unsubscribe
      // dpm($added_subs,'unsubscribe-$added_subs');
      Notifications_Subscription::delete_multiple(array('uid' => $uid), array('node:nid' => $node->nid), FALSE);
    }
  }
}