Line a 9x9-inch pan with foil. Place the cookies in a single layer in the bottom of the pan, breaking up the last cookie to fill in gaps.
In a small saucepan, combine sugar and butter substitute and bring to a boil. Once mixture is at a boil, continue boiling for 3 minutes, stirring constantly. Mixture should be a deep caramel color. Immediately pour over cookies and spread to cover completely.
Bake at 400°F 5 to 6 minutes. The mixture will look slightly bubbly.
Remove from oven and sprinkle chocolate chips over the top, and let sit a couple of minutes to melt. Carefully spread the melted chocolate over the cookies. Top with flaky sea salt.
Cool completely, break into pieces and enjoy!
Store at room temperature in a sealed container for up to one week.