From my understanding and as I have been accepted by EK, they do not write to your references until they atleast offer you the job. In most cases, and as I was notified at my assessment day, most of the time EK do not actually get in contact with your references, they only do so if they feel they need more information on you. In which case, you have nothing much to worry about in terms of getting in trouble with your manager. Hope that helps.
A