$email = new stdClass();
$email->subject = JText::sprintf('PAYMENT_NOTIFICATION_FOR_ORDER','eWAY','Accepted',$order->order_number);
$url = HIKASHOP_LIVE.'administrator/index.php?option=com_hikashop&ctrl=order&task=listing';
$order_text = "\r\n".JText::sprintf('NOTIFICATION_OF_ORDER_ON_WEBSITE',$order->order_number,HIKASHOP_LIVE);
$order_text .= "\r\n".str_replace('<br/>',"\r\n",JText::sprintf('ACCESS_ORDER_WITH_LINK',$url));
$body = str_replace('<br/>',"\r\n",JText::sprintf('PAYMENT_NOTIFICATION_STATUS','eWAY','Accepted')).' '.JText::sprintf('ORDER_STATUS_CHANGED',$order->order_status)."\r\n\r\n".$order_text;
$email->body = $body;
$this->modifyOrder($order,$this->payment_params->verified_status,$history,$email);
$this->modifyOrder($order, $this->payment_params->verified_status, $history, true);
It should fix your issue and send the email with the default content.