HVAC operation of PNNL models

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Obviously, this schedule is referenced by some objects in your HVAC systems. If you are working with a text editor try to search the schedule name and find objects that use this schedule. You cannot just remove or comment this schedule! If you want your HVAC systems to work all the time based on your ThermostatSetpoint:DualSetpoint change this schedule for all day types:

Schedule:Compact,
    HVACOperationSchd,   !- Name
    on/off,                !- Schedule Type Limits Name
    Through: 12/31,           !- Field 1
    For: Weekdays SummerDesignDay,            !- Field 2
    Until: 24:00, 1,       !- Field 4
    ...

But that's not very common. You can consider AvailabilityManager:NightCycle to turn on HVAC systems during unoccupied hours.