Line a 9-by-13-inch baking pan with parchment paper, leaving an overhang. Spread half of the crushed pretzels evenly in the pan.
Combine melted butter, brown sugar, and heavy cream in a saucepan over medium heat. Whisk constantly and gently boil for 4 to 5 minutes.
Remove from heat and stir in vanilla and 1 teaspoon sea salt. Cool for 5 minutes.
Pour the caramel over the pretzels. Add the remaining crushed pretzels and press lightly. Refrigerate for 15 minutes.
Melt chocolate chips and coconut oil in 30-second microwave bursts, stirring between each burst until smooth.
Spread the chocolate over the caramel layer. Add whole pretzels and the remaining sea salt.
Refrigerate for at least 2 hours. Lift from the pan and cut into 16 bars with a sharp knife.