Preheat oven to 400°.
Drain jalapeños. Cut 1/4 inch off stem ends of peppers, reserving stem ends. Carefully remove membranes and seeds, leaving peppers intact.
Combine cheeses in a small bowl. Spoon cheese mixture into a zip-top plastic bag; seal. Carefully snip off one bottom corner of bag. Pipe cheese mixture evenly into peppers; replace stem ends, pressing gently to seal.
Combine egg substitute and flour in a small bowl, stirring with a whisk. Combine breadcrumbs, garlic powder, salt, and paprika in a shallow bowl.
Working with one pepper at a time, dip in egg mixture; dredge in breadcrumb mixture. Repeat procedure with remaining peppers, egg mixture, and breadcrumb mixture. Return peppers, one at a time, to egg mixture; dredge in breadcrumb mixture. Place peppers on a baking sheet coated with cooking spray. Lightly coat peppers with cooking spray.
Bake peppers at 400° for 15 minutes or until lightly browned.