public Plan savePlan (Integer id, Plan plan )
    {            
        Department dep = entityManager.find( Department.class, id );
        List<Plan> newList = dep.getPlans();
        newList.add(plan);
        dep.setPlans(newList);
        return entityManager.merge( plan );
    }

where is mistake? It replace all plans connected to the department to the new one.

now doesn't help

it just change the name and data in database for plan related to this department and create a new relationship with plann and department