Heat 1/4 cup oil in large deep nonstick skillet over medium-high heat.
Add half of onions to skillet and saute until tender and golden brown, about 12 minutes.
Transfer onions to large bowl.
Repeat with remaining 1/4 cup oil and remaining onions.
Return all onions to same skillet.
Add vinegar and sugar, then cranberries, and simmer over medium heat until cranberries pop and juices thicken slightly, about 8 minutes.
Stir in chipotle chiles.
Season to taste with salt and pepper.
Cool.
(Can be prepared 5 days ahead.
Cover and refrigerate.
Bring to room temperature before serving.)
*Chipotle chiles canned in a spicy tomato sauce, sometimes called adobo, are available at Latin American markets, specialty foods stores, and some supermarkets.