I don't think that phrasing implying there was a whole brain instead of a part fares any better by tying it to a definition of fossil. It's not essential to the definition of fossil that what is recovered is a smaller subset of the whole thing. A fossil can be a fossil of an entire organism.

I think the that commenter's point is that the article makes numerous unqualified references to "the brain" which on a most natural reading would imply the whole brain when it's some (albeit very interesting) individual shards.