I can't speak for aust amateur slueth, but for myself, if the furniture had been moved after Dylan was missing, but before the first search warrant was issued, I would think someone was trying to cover something up or put something out of view.
But I am suspicious by nature. It would also depend on the person. I have a friend who moves the furniture every week. Makes me nuts that every time I go over, I have to look around to see where the chairs went, as I don't like sofas, in general.
In the case of this search warrant, though, I would think that between Mark appearing to not want to search Middle Mountain with Brandon (transcript over in transcript thread), being conveniently out of town during the the search where Dylan was found, yet saying he had been up to Middle Mountain to search on his own several times (links are over in the Media and Transcripts threads), and Dylan being found there, items they found on Middle Mountain would be cause for them to issue a new warrant, either to rule things out, or rule things in.