Bring water to boil in a large saucepan. Add chicken, garlic and thyme; cover and simmer until chicken is cooled through, about 15-20 minutes. Remove chicken and cool, then shred the meat. Reserve 1 cup of water for the sauce.
Heat a large skillet over medium. Add pumpkins seeds, stirring frequently, until they become fragrant and golden, but not brown (about 5-10 minutes). Set seed aside to cool.
Add vegetable oil to skillet and heat. Add jalapenos, onion, garlic and tomatillos; cook until softened, about 8 minutes. Place pumpkin seeds, tomatillo mixture, cilantro and 1 cup of reserved water in blender and blend until smooth. Return sauce to pan and season with salt. Cook on low heat for 10 more minutes.
Combine chicken with about a cup of the sauce and half the cheese. Fill tortillas with chicken mixture. Roll up and place seam side down in a 9 x 13-inch glass pan. Repeat with remaining tortillas. Pour remaining sauce over and spread until all tortillas are covered.
Sprinkle queso fresco onto enchiladas and bake for 25 minutes at 350°F Serve with lime wedges, cilantro and sour cream.