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In a mixer set to medium speed, cream together the brown sugar, butter, baking soda, vanilla and salt until light and creamy. Add the eggs, egg yolk and honey and beat at medium speed until well combined. Add the whey protein, cocoa powder, almond flour, oat flour, rolled oats, flaked coconut and chocolate chips and mix until just combined. Do not over mix, as this will toughen the dough.
Drop one heaping tablespoon of batter at a time, spaced about 3 inches apart, onto the prepared baking sheets. Bake for 9 to 10 minutes. Cool to room temperature on a rack and store in an airtight container for up to 1 week.
For the frozen yogurt: Add the Greek yogurt, milk, evaporated milk, peanut butter, honey and vanilla extract to a freezer-safe mixing bowl. Beat until smooth and well incorporated using an electric mixer. Cover and freeze. Re-beat every 30 minutes by hand or with an electric mixer. After 4 hours, swirl in the 1 cup of the mixed berry jam.
To assemble: Lay a cookie upside down. Top with a scoop of frozen yogurt, then sandwich with another cookie, pressing down gently to push the frozen yogurt out to the edges of the cookies. Place back in the freezer until frozen.