Adjust oven rack to lower-middle position and heat oven to 325 degrees.
Season beef with salt and pepper. Heat oil in Dutch oven over medium-high heat until shimmering. Add onions and ¼ teaspoon salt and cook, stirring occasionally, until well browned, 8 to 10 minutes.
Add tomato paste and garlic and cook until rust-colored and fragrant, about 2 minutes. Stir in flour and cook for 1 minute. Whisk in 2 cups broth, sugar, and 1 tsp thyme, scraping up any browned bits. Bring to simmer and cook until slightly thickened, about 3 minutes. Stir in beef and return to simmer.
Transfer to oven and cook, uncovered, for 90 minutes, stirring halfway through cooking.
Remove from oven and remove beef pieces to bowl. Add potatoes and carrots and cover with boiling water. Return beef to stew and stew to oven. Cook for 45 minutes.
Remove from oven and remove beef pieces to bowl. Add beans and cover with boiling water, if necessary. Return beef to stew and stew to oven. Cook for 45 minutes.
Continue cooking until beef and vegetables are tender, about 45-60 minutes longer.
Stir in 1/4 cup cold water mixed with 2 TBSP flour.
Add 1-2 tsp thyme, season with salt/pepper to taste, and serve.