What's the best way to seal unused flue?
You didn't mention what the opening was that the smell was entering the house with. If it is a thimble opening, you can block the opening with solid mineral wool insulation, cut to the size of the opening and fit snugly. This will stop the downward drafting. Add a thimble cap over the insulation and it will look fine. It also will stop cold air from entering the house through the flue.

You could also put a flat concrete patio block. cut to just larger that the flue opening, over the unused flue. You can secure it in place with some exterior masonry caulking. This will stop the drafting, but also make it possible to remove the cover if you decide to use the second flue for another purpose.