In a 3- to 4-quart pan over medium-high heat, shake and tilt sugar until melted and amber, 2 to 3 minutes. Immediately add vinegar, sautéed onions and garlic, and thyme. Stir until onions are deep amber, about 5 minutes.
Stir in wine. Let mixture cool to room temperature, about 20 minutes.
Put 1/2 the onion mixture in each of 2 plastic freezer bags (1-qt. size). Seal bags and freeze (see Cold Facts below).
Thaw 1 bag (see Thawing below). Pour onion mixture into a 3- to 4-quart pan and add 1 1/2 quarts chicken broth. Bring to a boil over high heat, stirring often; reduce heat and simmer to blend flavors, about 10 minutes.
Ladle soup into bowls and add 1 gruyère crouton to each. Season to taste with salt and pepper. Serve with remaining croutons.
Thawing: Cooking times are for thawed, chilled foods. Overnight: The night before serving, place container of frozen food in the refrigerator. Quick-thaw: Heat frozen foods in plastic bags in a microwave oven at 50% power just until pliable, then cook as recipe directs or empty food into a microwave-safe container, drape loosely with microwave-safe plastic wrap, and cook at full power (100%) until steaming. Note: If your microwave accepts metal, you can also quick-thaw dishes frozen in foil pans; follow manufacturer's instructions.
Cold Facts. Packaging: freezer bags. If ingredients include liquid, set each plastic freezer bag upright in a bowl, then fill. Squeeze out all air and seal bag. For better protection of frozen foods during storage, seal each bag inside a second one. Lay bags flat in freezer until solid so they will stack.