Preheat oven to 350°.
Place mushrooms in a food processor; pulse until minced.
Coat a large nonstick skillet with cooking spray; place over medium heat until hot. Add garlic and shallot; sauté 3 minutes. Add mushrooms; cook, stirring frequently, 8 to 10 minutes or until mushrooms are tender. Remove from heat; stir in cheese and next 4 ingredients.
Fill each phyllo shell with 1 heaping teaspoon of mushroom mixture. Place on a baking sheet; coat with cooking spray. Bake at 350° for 10 to 12 minutes or until phyllo shells are golden. Garnish with thyme sprigs, if desired.