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Preheat the oven to 350°F (176°C). Place the rack in the middle of the oven.
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Butter and lightly flour a 9 x 12 x 1½ inch (23 x 30 x 4 cm) baking pan. (preferably metal)
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Make a double boiler by placing a medium bowl resting on the rim of a 3 qt sauce pan filled no more than an inch (2.5 cm) of water. Turn the heat to medium-high and place the butter, semisweet chocolate and unsweetened chocolate in the bowl. Melt the chocolate and butter. Every now and then, carefully stir the chocolate and butter. Watch to make sure the simmering water does not touch the bottom of the bowl.
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Once melted, remove the bowl from the sauce pan and cool for 15 minutes.
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In a large bowl stir together the eggs, coffee granules, vanilla, and granulated sugar. Do not beat the eggs, just stir to combine.
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After the 15-minute cooling time, slowly add the melted butter and chocolate to the eggs and sugar mixture. Pour about a quarter of the chocolate into the mix and stir to temper the brownie mix. Slowly add the remaining melted chocolate and butter and stir at the same time. Once mixed together, allow the mixture to cool to room temperature. See note.
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In a medium bowl add the ½ cup (71 g) flour, baking powder, and Kosher salt. Use a small whisk and whisk the flour mixture until the flour, baking powder and salt are evenly combined. Add the flour mixture to the bowl with the cooled chocolate mixture and stir to combine. Toss the chocolate chips in the flour bowl with the remaining 2 TBS of all-purpose flour until they become nicely coated. Add the chocolate chips and flour into the chocolate brownie mix. Stir to mix.
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Pour the brownie mix into the prepared pan and spread to form an even layer.
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Bake for 35 minutes, or when a tooth pick inserted into the center of the brownies comes out clean. The edges will look slightly dry and just beginning to pull away from the sides of the pan. Do not over bake. The brownies will continue to bake while it is cooling.
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Remove the brownies from the oven and place on a cooling rack.
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When the brownies are just out of the oven, heat up your caramel sauce in a microwave until it thins out to a pouring consistency. Stir the caramel sauce until smooth.
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Evenly drizzle the caramel sauce over the hot brownies, then sprinkle with flaky sea salt.
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Completely cool the brownies before cutting into serving pieces.