In a medium bowl, whisk together the flour, salt and baking soda. In a separate medium bowl, add the sugars and lemon zest. Use your fingers to rub the zest into the sugar.
Tip the butter and the scented sugar into the bowl of a standing mixer. Using the paddle attachment, beat the sugar and butter until they turn light and fluffy -- about 5 minutes. Then beat in the egg and vanilla. At low speed, gradually beat in the flour mixture.
Detach the bowl from the mixer. Use a spatula to fold the chocolate chips into the dough.
Scoop 1-inch-diameter balls of dough onto an ungreased cookie sheet, spacing the balls about 2 inches apart. Pop the baking sheet into the refrigerator while you heat the oven to 350°F.
Bake in the preheated oven until the chocolate melts and the cookies color slightly -- about 8 minute for soft cookies, and 15 minutes for crisp. To avoid sticking, let the cookies cool on the baking sheet for 10 minutes. Transfer to a wire rack and let cool to room temperature.