Preheat oven to 375° and line two large baking sheets with parchment paper. In a small bowl, whisk together flour, baking soda, cinnamon, salt, and nutmeg.
In a large bowl using a hand mixer, cream together butter and sugars until light and fluffy. Beat in sweet potato, egg, and vanilla, then add dry ingredients and mix until just combined. Stir in chopped pecans.
Scoop 1” balls onto prepared baking sheets, 2 inches apart, and bake until golden and just set, about 10 minutes. Cool on baking sheets 5 minutes then place cookies on a cooling rack and let cool completely.
Make glaze: In a medium bowl stir together powdered sugar, syrup, milk, and pinch of salt. Drizzle glaze over cookies and sprinkle with chopped pecans.