Heat oven to 425°F. Spray 2 cookie sheets with cooking spray. Spray both sides of tortillas; place on cookie sheets. Bake about 3 minutes or until bottoms are slightly crisp; turn tortillas, and rotate pans. Bake 2 to 3 minutes longer or until bottoms are slightly crisp (tortillas will continue to crisp upon cooling). Remove tortillas to cooling rack; let cool. Reduce oven temperature to 350°F.
Meanwhile, in medium bowl, mix refried beans, salsa, chipotle chile and sauce.
Spread refried bean mixture (about 3 tablespoons) on each cooled tortilla to within 1/2 inch of edge. Top with pepperoni slices (3 per tortilla) and cheese.
Bake uncovered 6 to 7 minutes or until heated through and cheese is melted. Cut into wedges.