// $entity->items is m2m association

  /////////////////////
  // 1. Bug

  echo $entity->items->count(); // 2

  $entity->items->clear();

  echo $entity->items->count(); // 0

  $em->refresh($entity);

  echo $entity->items->count(); // 0 <-- ???

  //////////////////
  // 2. Workaround

  echo $entity->items->count(); // 2

  // remove items one by one

  $items = $entity->items->toArray();
  foreach ( $items as $item )
  {
    $entity->items->removeElement($item);
  }

  echo $entity->items->count(); // 0

  $em->refresh($entity);

  echo $entity->items->count(); // 2, as expected