Person 1: "I don't understand what it is about."
Person 2 wants to know what 'it' refers to. She could say "You don't understand what what is about?" or else "What is it that you don't understand what it is about?"
The first is natural but feels colloquial and only really functions in a conversational context. The second is awkward and I'm not sure if it's even grammatical. Is there another way of constructing this question?