I have been an invigilator for maths GCSEs and A levels, and before the exam started, we went round the hall with boxes collecting mobile phones, and other stuff that wasn't allowed in the exam - and we specifically asked for calculator cases/covers, because in some cases there were formulae printed on the inside of the case itself. The school should have done this, and then the note would have been collected before the exam started and there would have been no problem.
However, AngusOgg and others are right - your son's school teachers will have emphasised the exam rules over and over again, and he has little excuse for this absentmindedness. I hope that things come out as well as possible for him - which would be voiding that particular paper, I suspect.
However, I do think you should push to see the letter before it goes to the exam board, because your son's school should be taking a portion of the responsibility for this mistake - it shouldn't have been possible for him to keep his calculator case (as I said, when I invigilated, we never allowed them to keep the cases). If the school doesn't routinely collect the cases, then they are partly responsible, and should be making this clear to the exam board (though they may be very unwilling to do this because they won't want edexcel to think that they are lax in their procedures - that might risk their status as an exam centre). If the head invigilator stood up at the front of the exam and told all the candidates to hand in phones, calculator cases and any other prohibited material, and your son either didn't pay attention, or ignored the instruction, then he is in this on his own, I'm afraid.