Is there any way to connect a bone in the PHAT editor to something that it’s not already connected to? I use a weird skeleton for Hands and Feet that causes UE4 to not recognize that they’re connected, and whenever I simulate the skeleton it defaults to the Root position (0,0,0) and come disconnected from the skeleton.
Example:
creating constraints between the bone and the arm for some reason causes phat to think the constraint is between the root and the bone as well, which is super fun.
Thanks in advance, I will update this thread with any other answers to questions, and if I find a solution later on.
So I found a solution. It turns out that, even though the root bone doesn’t have a body attached to it, there were physics constraints attached to the bone. So solve this, I just had to create a body for the root bone, which exposed the constraints that were attached to it.
After that, all that was needed was to create a constraint between my hand and my lower arm, and everything worked as expected! You can see in the below gif that the hand on the left side (Robot’s Right hand) is attached to the arm when it falls now. 
Hopefully this helps someone else having the same issue in the future!
Now all I have to do is fix the weights and the joint angles… shudders