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I’m not entirely sure what’s happening in your scenario. But the combination of the HVAC Operation Schedule and Night Cycle Control will determine whether the fan runs under no load. For a VAV system the assumption is generally that they provide ventilation in addition to heating/cooling. Forcing the boxes to zero is not realistic since actual VAV boxes would never close completely (there would be risk of large static pressure variations if they did).

To get the behavior you're looking for I would suggest going to the "Control" screen and assigning some form of "Always Off" schedule for your "HVAC Operation Schedule" then set "Use Night Cycle" to "Cycle on full system if heating or Cooling required". This will in effect implement an "Availability Manager" and you can further adjust the settings of that if you wish.

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