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)).

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