Preheat the oven to 350°.
In the bowl of a standing mixer fitted with a paddle attachment, combine the all-purpose and whole wheat flours with the sugar, baking powder and salt. Add the butter and combine on low speed until the mixture resembles coarse crumbs, about 3 minutes. Add the molasses and 1/4 cup of water and mix until the dough forms a ball, about 2 minutes. Divide the dough into 2 equal pieces, pat each piece into a flat 4-inch square and wrap in plastic wrap. Refrigerate until firm, about 15 minutes.
Roll out each piece of chilled dough between 2 sheets of parchment paper into two 8-inch squares about 1/8 inch thick. Transfer each square, on the parchment, to a baking sheet; stack and freeze until firm, about 15 minutes.
Remove the top sheets of parchment and, using a pastry wheel or sharp knife, cut the dough into 2-inch squares (you'll get 16 cookies from each square of dough). Prick the dough all over with a fork and bake until golden around the edges, 15 to 18 minutes. Let the cookies cool completely on a rack, then break them apart into squares. Freeze 12 squares in a resealable bag until firm, about 15 minutes; reserve the remaining cookies for another use.
Place the chilled graham squares on a work surface and turn them bottom side up. Spoon about 2 tablespoons of the Fluff in the center of 6 squares, and about 2 tablespoons of the ice cream on the remaining 6 squares, then gently sandwich the squares together. Freeze until firm, about 30 minutes.
In a microwavable bowl, melt the chocolate chips in a microwave at 50 percent power for 3 minutes. Stir until smooth; let rest until cool to the touch. Dip the ice cream sandwiches in the melted chocolate, turning with tongs to coat. Place each bonbon on a parchment paper lined baking sheet and freeze until firm, at least 1 hour.