Depends on a few things. First, if it is JUST an air exchanger then yes, you have to reheat the incoming air (or cool it). If it is an HRV then those units recover much of the heat (cold) so that only a portion has to be reheated or cooled.
Most exchangers now are plumbed to the furnace to give distribution throughout the house so the fan will come on for that distribution.
My HRV is installed so that it can go throughout the house or only in the basement where all my tanks and cultures are, but I have to physically change the HRV output to just the basement or to connect it to the cold air return of the furnace.
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