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First off, EnergyPlus requires the first 16 fields (see the \min-fields in the energy+.idd file) of Daylighting:Controls which includes the the fields "Daylighting Reference Point 1 Name", "Fraction of Zone Controlled by Reference Point 1" and "Illuminance Setpoint at Reference Point 1". It doesn't make sense to have Daylighting:Controls without at least one reference point.
Setting fields in eppy to "" is not the same as deleting them. It has been a while since I needed to do that but I think you might want to create a new Daylighting:Controls object and just copy the fields that you want to the new object and then delete the old object.