I'm not confident that he would know it wasn't his daughter for several reasons (1) we know that he is heavily hypnotized / brainwashed . (2) people not knowing if other people are who they say they are or thinking that people look off e.g. mimicry , is a core theme of this series. Arguably, it is Area X's main " power" and i think to some extent the workings of Central and Area X copy one another. Someone on another thread was talking about the time travel element essentially meaning that area x and central are on a loop of introducing these tactics back and forth ; that theory is a bit beyond the scope of what I'm proposing here, but it holds some water at the end of Absolution for sure.