Passengers will still have to get to Goeshenen, to take the (shuttle) train to Andermatt, to connect to the line between Chur and Brig via Andermatt--the new tunnel bypasses that whole area. So, I'm assuming that the old route will not be totally shut down.
I'm guessing the majority of the trains will use the new route, with the old route as a (sort of) local service.
I found a PDF somewhere (Can't find it again) that states that the old line will have hourly local service. Which will also require a change of trains. So doable, but not as easy as it is at the moment with multiple trains per hour all with different sources going through the route.
We will have luggage, so the less number of connections we make from Lucerne on the way to Como the better.