Preheat the oven to 350 degrees . Grease a 12-cup muffin pan. In the top of a double boiler set over 1 inch of simmering water, melt 6 oz. chopped 1 chocolate and 1 1/2 sticks butter, stirring often, until smooth, about 3 minutes. Remove from the heat, whisk in the sugar and let cool for 10 minutes. Whisk in the eggs and vanilla, then the cocoa powder.
Spoon the mixture into the prepared muffin pan, filling each cup about two-thirds full. Bake until the cupcakes are cracked on top and springy to the touch, 18 to 20 minutes. Let cool in the pan on a rack for 10 minutes, then invert onto the rack to cool completely.
Slice the remaining 6 tbsp. butter into 6 pieces. In a microwavable cup, melt the butter, the remaining 3 oz. chocolate and the corn syrup at 1 medium power (50%) for 1 1/2 minutes; stir. Heat 30 seconds more; stir until smooth. Let the glaze cool for 10 minutes, then dip the bottom of each cupcake into the glaze. Let stand, glazed side up, for 5 minutes. Sprinkle with flaky salt and let stand until set, about 1 hour.
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