Combine flour, salt, pepper, and thyme in a bowl. Toss beef cubes in the flour mixture.
Heat olive oil in a Dutch oven or large pot over medium-high heat. Working in batches, brown beef cubes on all sides. Combine browned meat, apple cider, water, and cider vinegar in the pot and bring it to a boil. Add bay leaf; reduce heat to low. Simmer, partially covered, for 1 hour.
Stir in carrots, potatoes, onions, celery, and apple and simmer until the vegetables are tender, about 1 hour more.