Hi
Any separation is going to be difficult for a child to understand. I can remember going through similar trauma's when my father died, and I couldn't understand why my father had left me. Unfortunately at that sort of age many of us still have the illusion that the world revolves around our needs and it is difficult to understand that our parents are people too with needs and problems of their own.
For me, for many years afterwards I suffered from fear of abandonment so the first thing is to make sure that he understands that he is still loved and wanted.
I think there are several other things that you can do to help him, although I warn you that not all of them are easy, and indeed not all of them may be possible to do.
The first may be difficult for you, but it is to make sure that he understands that even if you don't fully understand why your partner is doing this that you support his/her right to do it, if it is really what he/she wants to do. Children are very perceptive and they will pick up your feelings. If you son gets the impression, even rightly, that you don't support what is happening then that will make it worse for him, because he will have to deal not only with his sense of loss, but also with the idea that half of him - the half that came from daddy, is inherently bad! Somehow, even though it may break your heart, you have to convince him that you can understand, at least to some extent, why his daddy might feel as he does, and that although it is difficult to understand, it is not a rejection of you and him.
This brings us to the second thing which is to find an area in life where your son longs for something, and something else which he already has but which you know he REALLY values. Then ask him to imagine what it would be like if he had to choose between the thing he has that he really loves, and the the thing that he longs for but does not have. Then explain that that is what daddy is going through. He is torn between two things that he really wants.
Thirdly I think you can explain to your son, that your partner will always be his daddy, even if he/she eventually looks a little different. Perhaps try to explain it in terms of re-decorating a room - it is still the same room even if it looks a bit different. His father will always be his father.
Finally and perhaps most importantly if you really want to help him, you can ask yourself whether there is any way that the two of you can stay together. Strangely enough there are many many partners who do stay together you know. You probably hear of more who split, but those who manage to make the adjustment often discover deep aspects of their love that they never expected.
Ah - yes but I am not a lesbian you may say. So ask yourself this - yes sex is a part of a relationship - but just how much of it? Did you just get married just to have a sex life? Was it just a thing of lust? Or were there shared values and shared interests? Were you not good friends before you were lover? And does not the personality that you were attracted to largely remain the same irrespective of the downstairs plumbing arrangements?
I had to ask myself this when after years of assuming that I would settle with a man life eventually produced a woman partner for me. I concluded that a true marriage was about far more than what goes on between the sheets, and so even if our initial physical contacts were a bit hesitant and unsure, the rest of the relationship was far more important.
Eventually the physical did come along, but our relationship rests on the friendship and not the physicality, and so can yours too IF you really love your partner. You wouldn't divorce him just because he became disabled would you? So how is this different?
Yes I know there is an issue of whether you were told at the outset or not, but the problem is that someone can only tell you about a problem if they have accepted that they have it, and most people like this have it so repressed that often they aren't even fully aware of what it means, so they CANT tell. Likewise someone destined for a wheelchair can hardly warn their partner that in six years time they will have a crippling accident. But in the one case the partner bravely stand by her incapacitated lover, and in the other she concludes that the relationship is over, even though they maybe more of the old person left than there would be if he was suddenly in a wheelchair.
I don't want this to seem like I am trying to be unsympathetic, because I am not. This is a shock for you. So these are just my thoughts and they may not resonate - in which case please just ignore them, but I hope I may at least have started you thinking.
Oh and just so you can understand where I am coming from, I am a postop Mtf who originally transitioned in my childhood, has been postop for several decades, and who is also the life partner of another postop MtF. So in a real sense I am both of you. I have a trans history myself, and I am an SO.