I think that the breakup of the family reflects the seismic effect of Bruno's disappearance. When he disappears, his mother and sister leave for Berlin, convinced that he would have gone there. His father remains at Auschwitz and searches for his son. In the end, this shows the effect that Bruno's disappearance has on his family. They could not progress with their life as if nothing had happened. Bruno's role in the family and his absence created such a great hole that the family experienced fragmentation. Boyne creates a setting in which Bruno's importance is accentuated when he disappears. It is at this moment that the Holocaust has become a personalized reality for the family, something that the father already knows and recognizes in his revelation.
Bruno's absence enables the pain of the world constructed by the Holocaust to be realized in the most intense of manners. It is for this reason that his disappearance has a profound impact on the family at the conclusion of Boyne's work. It is in this light that the effect of Bruno's disappearance is extremely significant in the narrative. When Bruno leaves, the sense of transcendence from the world disappears with it. The reality of the world comes crashing down on the family, resulting in the family's scattering apart from one another.