Start by slicing the ends off of the onions and peeling them. Slice them vertically in half, then slice each half thinly into half-moon shapes.
In a large dutch oven, melt the Earth Balance over medium-low heat. Add in the onion and sprinkle with some salt. Cover and let them sweat for 45 minutes.
Uncover, stir and sprinkle with a little more salt. Increase the heat to medium and saute for 45 minutes more, or until a rich caramelized color is achieved.
Sprinkle the onion with flour and stir well for about a minute. Add in the sherry to deglaze the pot and then throw in the thyme sprigs and bay leaves. Slowly pour in the stock and add the Not-beef bouillon cube. Simmer for about 10 minutes more. Remove the bay leaves and thyme.
Ladle the soup into small crocks and place a toasted baguette on top. Sprinkle with some of the Daiya and place into a 400-degree oven to melt for about 7 minutes. Remove and serve immediately.