A) Prolines have a virtual atom. I forget its name but I think it’s NV. Anyway, your coordinate reset is probably not resetting the virtual atom, so it remains out of place. The only thing the virtual atom is used for is to check its overlap with the proper backbone atom (probably N), so the only score that goes haywire is pro_close. Prolines aren’t rings in the atom_tree because the atom_tree is a directed acyclic graph (no rings!)
If you are resetting entire poses, why not just use an equality operator? Is there not one for poses? Perhaps python problematically forces shallow copies when you want deep copies?