I'm about to replace the furnace in our house. The existing furnace uses a 6" stack through the roof. I know most new furnace installations just use PVC and poke out of the wall at about ground level. Question is, can I reuse the existing stack since it's already there? Or are we better off sealing it up and forgetting about it. I'd rather not go through the wall if possible just because we have a deck right on the other side of the wall where the furnace is located.
The problem with reusing non-HE (High Efficiency) exhaust for a HE appliance (furnace or water heater) is that HE exhaust gases are much more acidic and humid than non-HE exhaust.
This means that for typical galvanized steel exhaust, a HE appliance will cause corrosion in short order, eventually perforating the stack, causing leakage of exhaust into the house.
The use of PVC in HE appliances is simply cost - PVC pipes are cheap, and the temperature of HE exhaust is low enough to allow for PVC to be used without melting (although there is some controversy around that, especially if the PVC pipes pass behind finished or through otherwise confined spaces). The other alternative is stainless steel, which is much more expensive.
If your existing exhaust stack is stainless steel, you should be able to reuse it for a HE furnace. If it's the more typical galvanized steel, your best bet would be to abandon it and run a new PVC exhaust stack. Going through the wall is typically the shortest path (and is allowed for HE exhaust), but depending on the installation you can also run the exhaust through the roof, perhaps even re-using the existing exhaust path.
When I installed a HE furnace (which replaced a non-HE one), the contractor ran about 12 feet of PVC pipe to move the exhaust on the exterior wall away from the power and gas meters, so in your case you could probably ask them to place the exhaust away from your deck. It all depends on the nature of the installation (finished/un-finished area, location of furnace in relation to the walls/roof, etc.).
You cannot use the flue in it's current state. High efficiency furnaces exhaust less heat out of your house. The exhaust gas is cool enough that it condensates that's why it needs a drain and also why the exhaust pipe is PVC The condensate is slightly acidic and will corrode even some types of stainless steel overtime. You can however, use the old flue as a chase to run your PVC pipe through. It's not easy but if your house has the furnace located in the middle in a finished basement, it's sometimes the only option.