RDKit is very fussy when it comes to inputs in SDF format. Using the SDMolSupplier, we get a significant rate of failure even on curated datasets such as the PDBBind refined set. Pymol has no such scruples, and with that, I present a function which has proved invaluable to me over the course of my DPhil. For reasons I have never bothered to explore, using pymol to convert from sdf, into mol2 and back to sdf format again (adding in missing hydrogens along the way) will almost always make a molecule safe to import using RDKit:

from pathlib import Path
from pymol import cmd

def py_mollify(sdf, overwrite=False):
    """Use pymol to sanitise an SDF file for use in RDKit.

    Arguments:
        sdf: location of faulty sdf file
        overwrite: whether or not to overwrite the original sdf. If False,
            a new file will be written in the form <sdf_fname>_pymol.sdf
            
    Returns:
        Original sdf filename if overwrite == False, else the filename of the
        sanitised output.
    """
    sdf = Path(sdf).expanduser().resolve()
    mol2_fname = str(sdf).replace('.sdf', '_pymol.mol2')
    new_sdf_fname = sdf if overwrite else str(sdf).replace('.sdf', '_pymol.sdf')
    cmd.load(str(sdf))
    cmd.h_add('all')
    cmd.save(mol2_fname)
    cmd.reinitialize()
    cmd.load(mol2_fname)
    cmd.save(str(new_sdf_fname))
    return new_sdf_fname