I have a forced-hot-air gas furnace set up to serve two heating zones. Zone 1 works fine, but the heat in the zone 2 rooms persistently smells like hot dust (like when a heating system is first turned on for the season, only this smell never quits). After 2 or 3 days sitting in this smell we start to feel sick and have to vacate or turn off that zone. I looked at the furnace and noticed that there is a bypass duct installed between the output plenum (where heated air gets distributed to the two zones) and the input plenum (where the return ducts bring room air back to the furnace input). There is an electric flapper valve in this duct. When zone 1 runs, this bypass valve is closed thus isolating the output from the input (though it opens immediately when the thermostat turns the furnace burners off). But when zone 2 runs, the bypass valve is open, allowing some of the heated air to immediately recirculate into the furnace input for additional heating. Is this normal? I suspect that this is wrong and is allowing the air in the output plenum to get too hot and causing the heating smell in zone 2 by overheating materials in the ductwork. What is the normal purpose of this bypass? The only thing I can guess is that it prevents temperature over-shoot in the rooms being heated by cooling the furnace down using re-circulated duct air rather than delivered air. Any thoughts are appreciated.
I'm guessing that your second zone is much smaller than your first. A bypass damper is used when the smaller of the two zones runs by itself. Without the bypass, if only zone two is calling for air you will have so much air goiung to that zone, it will sound like a hurricane. The damper takes some of that air and recirculates it to prevent this. As Beenthere says it also helps temper the hot air.
As to what your smell is, I can't comment. I must say however since it is a gas system and you say that it makes you sick, you should get an expert there PRONTO.