If they blocked off half the airflow that the unit is supposed to be supplying then they may be buying a new Unit soon anyway. May as well open some drywall and connect the upstarts vents to a new duct and put in a small furnace. You will probably want to dump the extra air from the original furnace into the downstairs (or whatever location you end up making it serve) so you don't choke it out. It will still be over sized for the job but at least it would have the airflow that it needs.
It's not a small job but depending on the house layout it might not be too bad either. You won't really know until someone goes to look at it. We can't tell you how big or small the job is without seeing it.
You will need space for the second furnace, your gas line will need to be big enough to accommodate the added Supply, you will need to have enough room on your existing electrical supply or run a new wire, pull down the drywall and run additional duct, don't forget about the return air. All this will take space to install and calculations to determine feasibility. If going with gas then you need the space on the wall or in the chimney to run additional flu vents. There are limitations as to where it can be placed so that will take some consideration also. If going with a high efficiency furnace then you will need access to a drain or install a pump.
In short, the job could be big or it could be small depending greatly on the access to the ducts, space available, and existing gas and electrical lines.