Preheat oven to 375 degrees. Spread pecans in crust. In a small bowl, toss chocolate chips in a little flour to coat, then scatter evenly over pecans. In a medium bowl, stir together eggs, brown sugar, corn syrup, vanilla, butter, and flour until well combined. Pour filling over pecans and chocolate chips.
Bake until filling is set and crust is browned, about 70 minutes. (If pie browns too quickly, loosely tent with foil.) Let cool on a wire rack at least 1 hour. Serve warm or at room temperature.