Preheat the oven to 350 degrees. Line two baking sheets with parchment paper.
Combine the flour, cornstarch, baking powder, baking soda and salt in a small bowl.
Whisk until well mixed. Set aside.
Add the vegan butter, brown sugar and white sugar to the bowl of an electric mixer. Beat on medium speed for 3 minutes until the mixture is light and fluffy. Scrape down the bowl.
Add the flax egg and vanilla extract and beat 60 seconds more.
Turn the mixer to the lowest speed and slowly add the flour mixture. Stir until just combined.
Remove the bowl from the mixer stand. Add the semi-sweet chocolate chips, milk chocolate chips and pretzels. Fold them in with a spatula taking care not to overmix and break the pretzel pieces.
Scoop the dough into 1⁄4 cupfuls. Make an indentation in the center of each and place a caramel piece inside. Close the dough over the caramel.
Place the cookie dough ball onto your prepared baking sheet spaced 3 inches apart.
Flatten the dough balls slightly, so they resemble hockey pucks. They should still be quite thick. Place 1-2 caramel pieces on top of each cookie.
Bake in a preheated oven for 12 minutes until edges are just set and the centers are still very soft. Remove from the oven and sprinkle immediately with sea salt. Cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.
Store cooled cookies in an airtight container at room temperature.