Preheat oven to 375 degrees F (190 degrees C). Grease a 12-cup muffin tin or line cups with paper liners.
Combine crushed bran flakes, whole wheat flour, sucralose, ground flax seed, all-purpose flour, baking powder, ground cinnamon, baking soda, and salt in a bowl. Make a well in the middle of the mixture.
Whisk egg whites together lightly in a bowl until foamy. Mix in buttermilk, honey, and applesauce. Pour mixture into the well and blend batter until just moistened. Fold in cranberries.
Fill muffin cups 3/4 full with batter; sprinkle tops with whole flax seeds.
Bake in the preheated oven until tops spring back when lightly pressed, 12 to 15 minutes. Cool in the pan for 5 minutes; transfer to a wire rack to cool completely, about 15 minutes.