Using an electric mixer or stand mixer fitted with the paddle attachment, mix the cream cheese on medium-high until smooth and creamy.
Beat in the sugar and flour on medium-low speed, scraping down the sides and bottom of the bowl. Mix again, if necessary, until there are no lumps.
Add in the sour cream and vanilla. Blend until smooth and creamy. Scrape down the sides of the bowl.
With the mixer on low, add in eggs, one by one, until fully incorporated. Stop when the mixture is fully combined. Overheating (mixing) adds excess air into the batter, which can cause cracks in the cheesecake.
In a medium bowl, heat chocolate chips in the microwave in 30-second increments, stirring as needed until melted and smooth. Stir 2 cups of the cheesecake batter into the melted chocolate; mix gently until incorporated.
Pour the vanilla cheesecake batter on top of the pecans and crust. Drop spoonfuls of the chocolate batter over the vanilla batter. Then, swirl with a knife or an offset spatula.
Bake until the top of the cheesecake turns golden (60-70 minutes). The cheesecake is done when 2-3 inches around the outside is set and barely puffed and the middle barely jiggles. The internal temperature of a baked cheesecake should read 150°F (and no higher than 160°F or cracks will form and texture will be tough).
With the cheesecake still in the oven, turn off the oven and crack the oven door. Let the cheesecake cool in the oven for about an hour. Next, remove it from the oven to cool on a wire rack until it is at room temperature. Then, place the cheesecake in the refrigerator for a minimum of 4 hours.