A great question. I had never noticed this potential contradiction. When I find such potential or apparent contradictions of a doctrinal or theological nature, I like to begin by assuming that there is a reasonable explanation (there always is!) The Bible deserves the benefit of the doubt with any claim of contradiction. Then, I ask myself which of the two passages is the more fundamental truth of Christianity? In this case, I believe that John 12:47-48 is the more fundamental truth, and we must interpret John 9:39 in light of the first passage. Before I do this, let me give you another example of this principle of interpretation.
My other example is when we compare Ephesian 2:8-9 (we are saved by faith, not by works) with James 2:24 (You see that a person is considered righteous by what they do and not by faith alone). In this case, I am convinced that Ephesians 2:8-9 is the more fundamental truth, and I interpret James 2:24 in light of Ephesians 2:8-9. In other words, the fundamental truth is that we are saved by faith, not by works. No work can save us. No work can remove the consequences of our sin. So, what does James 2:24 mean? It means that the kind of faith which saves us is the kind of faith which includes deeds. The kind of “faith” which is not accompanied by deeds is not the kind of faith that saves us. The fact that we are not saved by faith, does not mean that God cannot require work in order to be saved. God requires us to believe, which is a work, according to Jesus (John 6:29), in order to be saved. Ephesians 2:8-9 does not teach Luther’s “faith alone.”
Now, let me apply a similar approach to John 9:39 and John 12:47-48. I believe, like I already said, that the more fundamental truth is John 12:47-48. Therefore, we need to ask what Jesus said in John 9:39 means, in light of the fact that Jesus did not come in the body in order to judge people. His purpose in coming was to save, not to judge. So, what does he mean when he says, “For judgment I have come into this world, so that the blind will see and those who see will become blind.” Here is what I believe Jesus means in this passage. What Jesus is saying is that how people respond to Jesus will determine who is blind and who sees. He is not talking about final judgment. He is saying that we will be able to recognize who is blind and who can see based on how people respond to Jesus. This is how we will know who is blind and who can see. Our response will be our judge. Jesus did not come to judge. Judgment will happen later. Jesus came to save. However, our response to Jesus will determine where we are at now with God and where we spend for eternity. That is what he is talking about in John 9:39.