Posting this as a known issue. The hydrogen isotope-induced chirality is out of the scope of information in our current REMARKS section in the ligand PDBQT file. But this is more of an RDKit limitation.

Based on: rdkit/rdkit#7410
It seems like the chirality tags (@, @@) in Smiles can't be used for (hydrogen) isotope-induced chirality.

Version of RDKit: 2024.03.4

I tried (O)[C@@]([3#1])([2#1])C and (O)[C@@]([3H])([2H])C. Neither is a valid Smiles for Chem.MolFromSmiles at the moment.

I don't have a quick walkaround.

This is related to #295. Could not be fixed by #296.