Chicken Braised with Bacon, Onions and Riesling

12 red or white boiling onions 

1 chicken, about 4 lb. 

1 1/2 tsp. kosher salt, plus more, to taste 

1/2 tsp. freshly ground pepper, plus more, to taste 

4 thick-cut bacon slices 

12 small carrots 

2 shallots, minced 

2 Tbs. cognac or other brandy 

2 cups Riesling 

3 Tbs. unsalted butter, at room temperature 

3 Tbs. all-purpose flour 

1 1/2 tsp. chopped fresh thyme