In a 10- by 15-inch pan, broil poblano chilies 4 to 6 inches from heat, turning as needed, until skins blister and blacken all over, 15 to 20 minutes.
When chilies are cool enough to touch, gently pull off and discard skin. Cut a lengthwise slit through 1 side of each chili. Gently scoop out and discard seeds and veins; leave stems on chilies.
In a bowl, mix orange juice and lime juice.
Peel and pit avocado. Cut into 1/4- to 1/2-inch chunks and add to bowl. Add jalapeño chili, green onions, cilantro, and pomegranate seeds. Stir gently to mix salad. Add salt to taste.
Lay chilies on plates, slit side up. Spoon equal amounts of salad into each chili; some of the salad will overflow. Sprinkle cotija cheese evenly over stuffed chilies.