Preheat the oven to 425°F. In a large roasting pan, toss the onions, shallots, thyme sprigs, and olive oil. Season with salt and pepper.
Roast, stirring and scraping down the pan every 10 minutes, until softened and golden brown, 50–60 minutes, continue with 10 minute increments if they aren’t yet golden.
Discard the thyme sprigs. Add the wine and vinegar, scraping up any browned bits from the pan. Return to the oven and roast for another 15 minutes, until deeply caramelized. Spread onto a baking sheet to cool.
Finely chop the cooled onion mixture, reserving 2 tablespoons for garnish.
In a medium bowl, mix the onions with sour cream, chives, and yogurt. Season with salt to taste. Transfer to a serving bowl, top with the reserved onions, thyme, and everything seasoning. Serve with potato chips.