I'm surprised that the Smithsonian article didn't note that one of the problems in locating Jone's remains was that the burying ground had been used to inter the Swiss Guards that the Paris mob killed a few days later in mobbing the king's palace. I gather there was a solid layer of human bones covering earlier burials.
Not to mention all the trash over THAT layer.
I haven't read the whole article again, but IIRC they tunnelled under rather than excavating from the top down -- so probably never encountered the remains of the Swiss Guards.
Must have been a helluva rotten job.