My friend and I both retried this. But this time we used characters that had never done that story episode before and at every point where there was dialog we talked to the required NC one at a time (note the second to do so usually doesn't get the same response) waited a bit after all dialog had finished to make sure, and only then we progressed to the next part of the episode. This time we both successfully got credit for the Shining Blade part and boat worked correctly. So there is a flagging bug sometimes doing it on a character who has already done the story, which the devs are not fixing. So this should work as a workaround.