A) Rosetta’s energy functions are not likely smart enough to know what to do with the deprotonated LYS anyway – the standard energy function doesn’t have explicit electrostatics. I believe the explicit electrostatics terms will work properly with a deprotonated lys.
There is a deprotonated lysine with the residue type name LYS_D at (database)/chemical/residue_type_sets/fa_standard/residue_types/protonation_states. I don’t know the names for the python commands, but after reading your pose in, you should be able to do something like replace_pose_residue_copying_existing_coordinates(pose, position, LYS_D ) (it’s in core/chemical/util.hh)