Pour 1½ cups water, orange juice, lemon juice, vinegar, and soy sauce into a saucepan and set over medium-high heat. Stir in the orange zest, brown sugar, ginger, garlic, chopped onion, and red pepper flakes. Bring to a boil. Remove from heat, and leave to cool.
Place chicken into a re-sealable plastic bag. Pour 1 cup of sauce into bag. Reserve the remaining sauce. Seal the bag, and refrigerate at least 2 hours.
In another re-sealable plastic bag, mix the flour, salt, and pepper. Add the marinated chicken pieces, seal the bag, and shake to coat.
Heat olive oil in a large pan. Brown the chicken on both sides. Drain on a plate lined with paper towels, and cover with aluminum foil..
Wipe out the pan, and add the sauce. Bring to a boil, mix together the cornstarch and 2 tablespoons water and stir into the sauce. Reduce heat, add the chicken pieces, and simmer for about 5 minutes, stirring occasionally.