Preheat oven to 350°F. Lightly coat a 9-inch square baking pan with cooking spray. Line bottom and sides of pan with parchment paper, leaving a 1-inch overhang on all sides. Coat parchment with cooking spray; set aside.

Stir together brownie mix, melted butter, vanilla, ½ cup of the pecans, and ¼ cup of the evaporated milk until smooth (batter will be very thick). Press about 1 ½ cups of the brownie mixture into an even layer in prepared pan.

Bake in preheated oven until just set and still a bit gooey, 7 to 8 minutes. Let cool 10 minutes.

Meanwhile, place caramels and remaining ½ cup evaporated milk in a microwave-safe bowl. Microwave on HIGH in 1-minute intervals, whisking after each interval, until caramels are melted and mixture is smooth, about 3 minutes total. Stir in salt until combined.

Pour caramel sauce evenly over baked brownie layer. Sprinkle with ½ cup of the chocolate chips. Crumble and sprinkle remaining brownie batter evenly over caramel and chocolate (there will be caramel showing). Sprinkle evenly with remaining ¼ cup each pecans and chocolate chips.

Bake in preheated oven until edges are set, about 20 minutes. Sprinkle with flaky sea salt, if desired. Let cool to room temperature on a wire rack, about 1 hour, 30 minutes. Cover with plastic wrap, and chill until firm, about 1 hour. Using excess parchment as handles, remove brownies from pan; cut into squares. Store in an airtight container in refrigerator up to 2 weeks.