Grind or crush the pretzels into crumbs. Pour into a mixing bowl with the melted butter, powdered sugar, 1 cup Sunbutter, and the vanilla. Mix well. Spread the mixture evenly into a 9x12-inch baking dish, pressing firmly.
Combine the chocolate chips with the remaining Sunbutter in a microwave-safe bowl. Microwave at 30 second intervals, stirring in between, until the mixture is melted and smooth. Spread the mixture evenly over the pretzel mixture. Refrigerate for at least 1 hour before cutting into squares.