Lay pork chops on a baking sheet, lightly coat with olive oil, then thyme, and sea salt and pepper to your liking. Rub the seasonings into the meat and set aside.
In a sauce pan, combine the brown sugar, cinnamon, nutmeg, water and apples. Bring to a boil, and then simmer for 20 minutes or until apples are tender. Combine the flour with a tablespoon of cold water to dissolve. Add flour mixture to the apples and return to a boil for 5 minutes or until sauce begins to thicken. If the mixture becomes too thick, you can add more water, and likewise, if it's too thin, you can add more flour-water.
Place porkchops in the preheated oven and bake for 20 minutes. Top the chops with the apples and return to baking for another 10 minutes.
This is great with steamed green beans, and is a healthy alternative to other apple pork dishes.