It does seem that the 4 eyes essentially become 2. We know for a fact from that chapter that you need the 4 eyes to gain the EMS. If you think about it, this means that the 2 original cannot be removed from the body. Since we know Madara gained the EMS and still had the appearance of 2 eyes, it must mean that the 4 basically became two by putting the 2 new eyes over his two old eyes. Of course, this does not make a lot of sense and the details have not been explained making it an ambiguous situation, but we have to assume from this chapter that a switch is simply not adequate for them both to gain EMS.