Eva Gklezakou,
I don't know the answer to your question. You can try applying night ventilation manager in the manner described and review the results. I pulled the 5ZoneNightVent3 input file and modified it by turning off cooling and heating coils using availability schedule.
Result below shows that space temperatures are not maintained at setpoint when the coils are off as expected but dampers are fully open for the modified case. Hope this helps.
Original input file, (Damper position on secondary axis)
After modification,