In a large bowl, combine oats, whole wheat pastry flour, almond flour, brown sugar and baking soda.
Mix together with a spatula and then cut the butter and milk in with your finger tips until the mixture is a "crumb" texture.
Pour about 2/3 of the mixture into a 8x8 or 9x9 baking dish and press down firmly with your hands or the bottom of a glass to form the base of the bars.
Layer the cheese slices on top with enough slices so that the crumb mixture is completely covered.
Lay the apple slices on top of the cheese.
Add the chopped pecans to the remaining crumble mixture and pour on top of the apples. Press down firmly again to form the top of the bars.
Bake for 35 minutes.
Remove from oven and let cool completely before cutting into bars.