Toss together the tomatoes, 1/4 cup oil, 2 teaspoons salt and black pepper. Spread the tomatoes in a single layer on a foil lined baking sheet. Bake 45 minutes.
In a large stockpot/dutch oven, over medium heat saute onions, garlic and red pepper flakes in remaining 2 Tablespoons olive oil and butter, for about 8 minutes. Once the onions have softened turn off the heat and add the Cognac. Be careful because the Cognac may flame as it burns off the alcohol. Turn the heat back on and let the liquid reduce a little, about 5 minutes.
Add the canned tomatoes, chopped basil, thyme, chicken stock, remaining 1 teaspoon salt and oven roasted tomatoes, including their juices on the baking sheet.
Bring to a boil and let simmer uncovered for 40 minutes.
Using an immersion blender or blender (in batches) blend the soup until it is silky smooth. If you use a traditional blender only fill the jar up by about 1/2 so the heat does not cause the soup to explode all over your kitchen.
Taste for seasoning and adjust if necessary.
Serve hot or cold.
Notes:
* If using a blender be sure to allow some of the steam to escape while blending.