Season the beef with the salt and pepper.
Heat 1 tablespoon of the oil in a large heavy skillet over medium-high heat. Add the beef and cook until deeply browned all over, 12 to 15 minutes. Remove to a 5- to 6-quart slow cooker.
Reduce the heat under the pan to medium and add the onions. Cook until the onions are lightly browned, about 5 minutes. Transfer to the cooker. Add the remaining 1 tablespoon of oil to the pan, then add the celery and carrots. Cook until the vegetables are lightly browned, about 5 minutes. Add the wine, bay leaves, and thyme, simmering and scraping the bottom of the pan for a minute or two. Scrape the pan contents into the slow cooker and pour on the broth.
Cover and cook on low for 6 to 8 hours. Avoid overcooking the beef; a fork should slide in and out easily but the roast should not be falling apart.
Remove the roast to a platter and cover with foil to keep warm. Remove the bay leaves. Whisk together the flour and water in a cup until the flour is dissolved. Whisk the flour mixture into the liquid in the cooker and simmer on high until thickened, 5 to 7 minutes.
Slice the beef and serve with the sauce.
Tip: If the boneless roast doesn’t come tied, ask your butcher to tie it so it keeps its shape.