Heat 2 tablespoons canola oil in a large pot over medium-high heat. Add the brisket, season with 1 1/2 teaspoons salt and a few turns of black pepper and cook, turning, until browned on all sides, about 10 minutes. Reduce the heat to medium and add the onion, carrots and celery. Cook, stirring, until softened, about 10 minutes.
Add the wine and cook for a few minutes until it's reduced by half. Add the brown sugar, tomato paste, tomatoes, stock, rosemary and apples and simmer, uncovered and stirring occasionally, until the meat is tender, 2 1/2 to 3 hours. You want this to reduce and get quite thick and saucy; however, if it reduces too far and it's more gloopy than saucy, add a bit more stock.
Meanwhile, preheat the oven to 375 degrees F. Brush the innards of your squash with the remaining 1/2 tablespoon oil and sprinkle with 1/4 teaspoon salt and a few turns of black pepper. Roast cut-side up on a rimmed baking sheet until a fork pokes easily into the center, 1 to 1 1/2 hours. Scoop the squash flesh into the bowl of a food processor and puree until very smooth. Stir it into the brisket mixture and add the red pepper flakes. Taste and adjust the seasoning as needed.
Increase the oven temperature to 400 degrees F. Transfer the brisket mixture to a 9-by-13-inch casserole dish and top with the latkes lined up in nice neat rows. Bake until the mixture is bubbly and the latkes are deep brown, 20 to 25 minutes. Let cool slightly and then top with chopped parsley, if using.