I think it's the smiles parser that is losing the aromaticity, but I don't know.
SmilesParser smilesParser = new SmilesParser(
IMolecule molecule = smilesParser.parseSmiles(smile);
MDLV2000Writer m2w = new MDLV2000Writer(System.out);
I used my go to test molecule:
There are no coordinates in the ouput molfile so I could rule out sdg removing the aromaticity but the bond orders should still be ok I would assume.