I think what happened is the "bounding box" of the artwork changed, which changed CH's understanding of the center of the artwork, moving the origin. Yes, its a bit of a pain.
Rigging does get lost if you change the structure of the character above the layers you changed (e.g. introduce another level of grouping). But your diagram where it is offset makes me think its the above problem. One workaround is to create a big (independent) rectangle behind everything else so the size does not change. I personally just finish the artwork first (plan it out as best possible) then rig it.