Lower the oven temperature to 300°F (148°C). A gentler oven helps the cheesecake bake evenly without puffing too fast.
Beat the cream cheese, sugar, flour, and cocoa powder on low speed in a large bowl until smooth, stopping to scrape the bowl as needed. The mixture should look thick and creamy with no visible lumps.
Mix in the sour cream and vanilla extract on low speed until fully incorporated. The batter should loosen slightly and turn extra silky.
Add the melted chocolate in two additions, mixing after each one just until combined. This helps the chocolate blend in evenly instead of forming streaks or small firm bits.
Add the eggs one at a time, mixing slowly after each addition and scraping the bowl when needed. Stop as soon as the batter looks uniform, because too much mixing adds air and encourages cracks.
Spread about a cup of the cheesecake filling into the crust as the first layer. This base layer should cover the bottom evenly so the topping stays centered.
Spoon about 1 1/2 cups of the coconut pecan topping over that filling layer. Keep it gentle so the layers stay distinct instead of blending together.
Pour the remaining cheesecake batter over the topping layer with a light hand. The batter should flow over it and cover it without digging down into the center.
Set the springform pan inside a larger pan and pour warm water into the outer pan until it reaches halfway up the sides of the springform pan. The cheesecake pan should stay upright and the foil should remain above the water line.
Bake for 1 hour 25 minutes to 1 hour 30 minutes. The center should look set around the edges but still have a gentle wobble when you tap the pan.
Turn off the oven and leave the door closed for 30 minutes. This first cooling stage lets the cheesecake settle without a sudden drop in temperature.
Crack the oven door open and leave the cheesecake inside for another 30 minutes. The top should stay level as it cools slowly.
Remove the cheesecake from the oven and water bath, then refrigerate for 5 to 6 hours or overnight. It should feel firm and well chilled before you add the final topping and slice it.
Spread the remaining coconut pecan topping over the chilled cheesecake before serving. The topping should sit thickly on top instead of sliding off the sides.