The soul, on the other hand, does not have a physical component that we've found, so removing it would not necessarily result in any physical change (excepting the death of the target). Thus, the difference between the physical and the metaphysical object is relevant.
I think the reason you were downvoted is the fact that a very large proportion of people on this blog (including Eliezer) believe that if their is a separate component we could refer to as a soul (or consciousness, or any similar concept), that it is entirely contained within the real world - that is, it is going to be some component of the brain instead of any sort of separate metaphysical property.
I don't think it's fair to downvote you for that, since the opposite is clearly the prevailing opinion in the HP universe.
However, given Eliezers extensive arguments against any sort of epiphenomena, I think it is highly probable that it was the mention of the soul that should have set off alarm bells for Harry, because SuperRational Harry shouldn't believe in a soul, at least not without major caveats.
I think the soul question is going to come up in the eventual direct conflict with Voldemort, and that it is going to be a Very Big Deal. It is the source of Voldemort's immortality, after all. It's the most important question Harry needs to answer, and he hasn't even asked it yet.
Update: Discussion has moved on to a new thread.
The load more comments links are getting annoying (at least if you're not logged in), so it's time for a new Harry Potter and the Methods of Rationality discussion thread. We're also approaching the traditional 500-comment mark, but I think that hidden comments provide more appropriate joints to carve these threads at. So as of chapter 67, this is the place to share your thoughts about Eliezer Yudkowsky's Harry Potter fanfic.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six. The fanfiction.net author page is the central author-controlled HPMOR clearinghouse with links to the RSS feed, pdf version, TV Tropes pages, fan art, and more, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: