My understanding is that Shinji accepts this and returns with the knowledge. I'd assume with this knowledge, you would still have an AT field (since it retains his physical form), but I'm guessing the knowledge of this is sufficient to make progress. It's debateable that him returning is the true "evolutionary"/instrumentality step since he does come back better and with new knowledge. Perhaps instrumentality is just a test...hmm? (I just came up with that btw

Daniel ^_^