Sprinkle beef with 1 teaspoon of the chipotle chile pepper. Heat 1 tablespoon of the oil in Dutch oven on medium-high heat. Add beef; cook and stir about 10 minutes or until browned. Remove beef with slotted spoon.
Stir onion and bell pepper into the Dutch oven; cook and stir 3 minutes. Return beef to Dutch oven; stir in remaining 1 teaspoon chipotle chile pepper. Add squash, beef stock, tomatoes, brown sugar and cumin. Bring to boil. Reduce heat to low; cover and simmer 30 minutes, stirring occasionally.
Cook and stir flour in remaining 1 tablespoon hot oil in small skillet on medium heat 5 minutes or until golden. Stir into stew; cook, uncovered, 10 minutes or until thickened.