Reparenting joints after control rig build

Hey there

So I’m using the A.R.T. rigging tool to rig a biped character in Maya 2016.
I want to re-parent joints, now after the control rig has been build, hopefully without rebuilding the controls.

When I change the Export file (reparent inside the skeleton creation template, and re-position the joint in the skeleton placement template) it looks fine. When I save it and reload the reference on the AnimRig file, the joint is not positioned, and is stuck on it’s original creation point (in this case, a spine3 joint).

It seems that the build file is not reading the re-parenting of the joint.

Is there a work-around for this, or is this a bug?