I have to admit that I’m still running WordPress 2.9.1. Hence, the line numbers are probably different in your case, but it should be possible to find the place in the code where the relevant parts have been relocated. The more important question is whether WordPress has changed its behavior in this regard. This may be the case, according to this:
Change to comments UI to show when a comment is replying to another, and link to the parent commentHave you seen these parent comment links on other WordPress sites?