Keep your manufactories. You'll always need them. Later chapters may use more of the tier 2 and tier 3 goods, but you will definitely always need to have all of your boosted goods available. Even if you're going through a section of the tech tree that doesn't need as much, say, planks, you'll want them to trade and to save up for when you DO need them again. Would definitely recommend focusing on your boosted good at each tier rather than keeping a bunch of all three tier 1s, all three tier 2s, and all three tier 3s, but that's a play-style preference.
Plus, tournaments, province negotiation, and other special events will definitely drain your tier 1 stockpiles occasionally!