Is it permissible to continue working for an employer who owns a cigarette company, if I am asked to design packaging for their products, knowing that my salary comes from another of his businesses (engineering consultancy) and not directly from the cigarette company, and that my refusal to design might affect my job?

It is permissible to work in engineering consultations for the owner of a cigarette company, even if the salary comes from his mixed funds, because the prohibition of ill-gotten gain pertains to the liability of its owner, not to the money itself. However, it is not permissible to design cigarette packaging, as that falls under cooperation in sin. If refusing this affects the work, then it is not permissible to cooperate with him in what is forbidden, except out of the necessity of being compelled to remain in the job to provide sustenance, provided that the necessity is estimated according to its measure and ceases when it ceases.