What I've been able to piece together from the fragments of this case that have been reported by non-technical journalists is that he used some sort of P2P software like BitTorrent to download the files. This P2P software kept the checksums of every downloaded file on his unencrypted drive (basically it stored the torrent files somewhere). The FBI compared the checksums in those file to ones of known CP images and found some number of matches (how many has not been reported from what I've seen).

So it really looks like they've got plenty to convict this guy on the evidence they have, but are refusing to bring the case to trial until he unlocks his external hard drive for some reason.