The one in the lower tower isn't replaced because you get a couple copies from Eddie directly. I didn't want to remove it though because it was there in the original cell. I know it looks kind of odd having a space there, but I would have assumed you would shuffle things around a bit anyway to make yourself more at home.
The current beta version requires you to build the Trader at Raven Rock. The Prerelease version, and the eventual final release, removes that requirement and exchanges it for needing to choose between Falco and Carnius. Once you prove your loyalty to one or the other, they will arrange shipments to your tower for you. If they're both dead, then the third NPC who makes you Factor of the EEC will arrange shipments after completing the EEC questline. I wanted to open up the choices and make it available no matter how you play the EEC questline.
Finding the rest of the silver is kind of random, depending on time and when you wander into the Treasury after a certain period. I left the scripting local to kind of randomize the event rather than having a global script initiate it after X many days. The stuff you find in the chest doesn't automatically sort back onto the shelves, since they could be in your inventory or not at the time.