Thanks for the suggestions. I have been picking up skulls as well as bones. I did find one more bone hidden by a tree branch, and one behind a mountain peak.
I've now gone over the map systematically and repeatedly, looking at every tree, stump, ruined building, and rock and clicking on everything that looked even faintly like a bone or part of one. I've destroyed every one of my own buildings that looked as though it might be hiding a terrain feature.
I'm still one bone short to open the chest.
Is there anything else I can do, short of restarting the game altogether?