Add chopped apples, brown sugar, maple syrup, lemon juice, vanilla extract, cinnamon, nutmeg, and kosher salt to a medium-sized mixing bowl.
Stir to combine and let sit for 30 minutes. The apples should be sitting in a loose liquid after 30 minutes
Add the apple mixture with all its juice to a 12-inch skillet set over medium heat.
Simmer for 10 minutes or until the apples are soft but not falling apart. The sugar mixture will thicken up as well.
Remove the skillet from the heat and let cool.
Set out 4 (1/2 pint-sized) glasses and add one tablespoon of the apple mixture, 1/2 cup yogurt, one tablespoon apple mixture, one tablespoon granola, top with remaining yogurt and one tablespoon granola.
Continue until all the jars have been filled.
Store covered and serve within a day of making so the granola does not soften too much. If you leave the granola out you can save for 2 days.