Season the beef chuck cubes with 1/2 tsp each salt and pepper. Coat the pieces evenly so the seasoning stays with the meat through the braise.
Heat 1 tbsp oil in a large heavy-based pot over high heat, then brown one-third of the beef deeply on all sides and transfer it out. Work in batches with more oil as needed, listening for a steady sizzle rather than a watery boil.
Lower the heat to medium-high and cook the onion and garlic for 3 minutes in the same pot. The onion should soften and the garlic should smell fragrant without browning too quickly.
Stir the flour through the onion mixture until it coats the aromatics. This flour layer will give the finished gravy a velvety thickness.
Pour in the beef stock slowly while stirring, then add the wine, tomato paste, Worcestershire sauce, coarsely ground pepper, and bay leaves. Keep stirring until the flour dissolves and the liquid looks smooth rather than lumpy.
Return all browned beef and any collected juices to the pot, cover, and adjust the heat to maintain a gentle simmer. Small, lazy bubbles keep the meat moist while it slowly softens.
Cook covered for 1 hr 45 minutes, then uncover, raise the heat slightly, and cook for 30 - 45 minutes, stirring regularly. The beef is ready when a fork slides in easily and the gravy coats the back of a spoon while still coming just about up around the meat.
Remove the pot from the heat, cover the filling, and cool it completely before assembling the pies. Chilled filling should be thick and mound easily in the pastry shell without flowing toward the rim.