The obsidian prayer beads are missing. They were the last piece to be found, I had found the others and activated the base in camp. I found the location for the prayer beads, the beads were missing. This was during  the a path to the garden main story quest. I looked up the bug on other forums, and reloaded to an earlier save, to the animancy method. I went back to the location for the prayer beads and they were still missing. I bought the clue from the merchant as well. The earlier save has 1 piece, the later save has all but the prayer beads. 

I'm in the same situation.  Found the skeleton on the north side of the Glade but no prayer beads.