It is my opinion that an owl dined on your latest missing guinea. The owl will keep coming back until it gets the other guinea also if you continue to allow it to roost in the tree.
You should read the Raising Guinea Fowl 101 thread from the start and pay particular to posts made by PeepsCA...
Guineas are by their very nature wild birds. They are only semi-domesticated. Under ideal conditions or in their native land, guineas can and do survive in the wild. A lone guinea will not survive. They are by nature a flock bird and will seek others of their own kind. I don't know where...