If I had to speculate about this, I would say that Twain had probably finished saying what he wanted to say at that point. He had set up the main themes of the book by the end of this chapter. We already know at this point that Huck is conflicted about whether he wants Jim to be free.
At the end of this chapter, the themes are set up and you could imagine the novel stopping there, with us not knowing what would happen next. So I can imagine that Twain put it aside for a few years trying to figure out if he should leave it there, unresolved, or if he should write more. If he should write more, how should he finish it -- how should he resolve the conflict?