I'm in the process of testing my engine on a test stand before installing back into the car. There are 2 outlets on the bottom of the blower that originally had flappers. In my case they are long gone. How critical, if at all are these flappers?

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Thanks

They help with the heating system. If you want heat, add them.

Slight Hi-jack...

If you only have heat on the Drivers side should you cap the Passenger side or leave it?

I thought I read somewhere that the flaps close at idle speed, which helped circulate air directly to the engine. At the lower idle RPM range, the engine needs all available air to help cool the engine, as the car rev'd up in RPM, the flaps would open, directing air to the heat exhangers?

The flaps only close when the aux fan goes on to keep more air in the heat exchanger system. If you leave them off, your aux fan may not blow as hard into the cabin, but otherwise they're irrelevant.