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If I understand what you're asking correctly, then yes, I think it is the case that the AirflowNetwork window elements won't have an impact when the fans aren't operating. To get what you want you'll have to replace your previous infiltration objects with enough (AirflowNetwork) leakage to get about the infiltration you had before.

There are a lot of reasons the infiltration objects and AirflowNetwork are kept apart, but at a high level those infiltration objects are a load (outside air that needs conditioning) while AirflowNetwork is balancing inflows (which we can consider as loads) and outflows (not loads). That's glossing over a whole bunch of details, but that's the basic idea.