At times, you'll need to alter the fit of the hierarchy in the Physique mesh, or change its structure. To do so, you change the default, initial pose, which Physique uses as a reference for various operations, including reinitializing.
For a biped, you change the structure in Figure mode, then reinitialize the Initial Skeleton Pose.
For a Bones system with the HD IK solver, there is a Show Initial State check box in the Motion panel, on the IK Controller Parameters rollout.
For any other hierarchy, use frame 0 for the initial pose. Be sure your animation does not affect the position of the skeleton in frame 0.