Remove phyllo shells from package and place on a large rimmed baking pan.
Saute onion in a small amount of olive oil until tender; set aside.
In a glass measuring cup with a spout, combine eggs, cream, cheese, flour, salt & pepper and whisk until smooth.
Stir in sauteed onion and crumbled bacon.
Pour mixture into phyllo cups, filling almost to the top.
Bake at 350 degrees approximately 12 minutes or until eggs are set.
Garnish with chopped fresh chives.