In a large Dutch oven, heat 2 tablespoons olive oil over medium-high heat. Add the shallots and cook until golden and fried, about 4-5 minutes. Add the carrots and cook, stirring often, until carrots start getting tender, about 8 minutes. Season with salt and pepper, add garlic and cook one more minute. Remove the carrot mixture to a bowl and keep aside.
Place the flour in a shallow bowl and season with salt and pepper. Add 2 tablespoons olive oil to the Dutch oven. Flour the portobello chunks and place to brown in the Dutch oven. You may need to do this in batches, depending on the size of your pan. Once the portobellos are browned, place them all back in the pan, and add the Cognac. Stir to remove brown bits from the bottom of the pan, and let the alcohol evaporate. Add the wine, vegetable broth, bay leaves, and thyme. Bring to a boil, reduce the heat to a slow simmer and cook, covered, for 35 minutes, stirring occasionally.
While the mushrooms are cooking, blanch the cipollini onions. In a saucepan, bring some water to a boil. Place the onions in the boiling water and let cook for 2 minutes. Remove from the hot water and let rest until cool enough to handle. Remove the peel, once you can touch the onions.
After the 35 minutes cooking time for the mushrooms, add the carrot mixture, cremini mushrooms, and onions to the Dutch oven. Cook, stirring occasionally, for an additional 30 minutes, or until the carrots are tender, but still hold their shape. Season with sea salt and pepper, to taste, and cook for an additional 5 minutes.
Serve with fresh parsley, over garlic mashed potatoes, along with some crusty bread, to soak up all the sauce. Bon appétit!