Place brisket in a 5-qt. slow cooker; top with onion and bacon. Combine tomato sauce, pepper and salt; pour over meat. Cook, covered, on low until meat is tender, 4-1/2 to 5 hours.
In a microwave-safe bowl, combine refried beans, salsa and chilies. Microwave, covered, on high until heated through, 2-3 minutes.
Remove meat from slow cooker; when cool enough to handle, shred with 2 forks. Layer bean mixture, meat and cheese off-center on each tortilla. Fold bottom and sides of tortilla over filling and roll up. Serve immediately.
Freeze option: Individually wrap burritos in foil and freeze in freezer container. To use, partially thaw overnight in refrigerator. Preheat oven to 350°. Bake foil-wrapped burritos on a baking sheet until heated through. To reheat one burrito, remove foil and rewrap in damp paper towel; microwave on high until heated through, turning once. Let stand 15 seconds. May be frozen up to 2 months.