Pierce the potatoes with a fork on all sides (this will prevent them from exploding in the microwave!). Wrap each potato in a damp paper towel. Microwave a potato for 2 minutes, turn it over, and microwave for another 2 minutes. You want it tender, but not mushy. Repeat with the second potato. Set aside to cool for a few minutes while you prepare the rest of the ingredients. Once the potatoes are cool enough to handle, trim the ends and remove peels. Slice into ½-inch rounds.
Spray an 11-inch by 7-inch baking dish with cooking spray.
In a large bowl, gently toss together potato rounds, chopped apples, and 2 teaspoons flour. Add 1 cup of sugar and mix well. Place in prepared baking dish.
To prepare the topping, stir together oatmeal, pecans, ½ cup flour, brown sugar, melted butter and salt until completely combined. Sprinkle over the potato mixture.
Bake uncovered at 350 for 45 minutes, or until apples are very tender. If the topping starts to get too brown before the fruit is done cooking, just cover lightly with foil for the remaining time.
To prepare ahead: Follow instructions through step 3 (placing the fruit in the baking dish), cover, and refrigerate. When ready to bake, add the topping and bake according to directions above.