Hi,
It seems that there is a bug in the save_to_sdf function (SaveToSDF.py module). It does not save only 2D information even if the '2d_output_only' option is activated. The simple workaround is to change the "for" loop:
for m in contnr.mols:
if not params['2d_output_only']:
m.load_conformers_into_rdkit_mol()
w.write(m.rdkit_mol)
Best,
Alex