Sounds like you need a MASON to install a new thimble or opening in the chimney and close the old low one..........
And a HVAC mechanic/plumber to reconfigure the two vent ducts..........
In many 'towns' these may be the same person(s)...I would call your heating contractor to quote the job......The suggestion to vent out the window is pretty lame......I wouldn't want it there unless there were no other options.
The village inspector is worried that flue gases will re-enter the building because of the two different height flues...........doug