Correct, it's not the same nan. The best way I've ever seen of translating "nan desu" is by adding "You see, " at the beginning of the english translation. It doesn't work in the case of "sou nan desu". But the basic idea is to bring the speaker and listener closer together on a point of agreement. It adds "feeling" and "mood" to the expression, not just meaning. In English this can best be expressed through tone of voice.