Managed to find a working solution in the email archive: https://www.mail-archive.com/[email protected]/msg00172.html
sym.add_site_family(graphene.sublattices[0], other_vectors=[(-1, 2)])
sym.add_site_family(graphene.sublattices[1], other_vectors=[(-1, 2)])
where graphene is the honeycomb lattice and sym is for example sym =
kwant.TranslationalSymmetry((-1, 0)).
