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Preheat oven to broil setting. Line a baking sheet with foil if desired and spray with cooking spray.
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Heat butter in a small saucepan over medium heat. Add shallots and thyme. Season with salt and pepper. Cook shallots, stirring continuously, until shallots begin to soften and caramelize, 4-5 minutes. Remove from heat and set aside.
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Place bread in skillet to soak up any butter and juices left over from the shallots. Transfer bread, wet side down, to prepared baking sheet.
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Top each slice of bread with sliced apples. Then layer 1 ounce cheese. Lastly, evenly divide shallots between sandwiches.
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Broil for 3-5 minutes or until cheese is melted and bubbly.