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There is a similar issue in this question response by @keigo. https://unmethours.com/question/55005/hvac-energy-consumption/#55304

"if you want to model the multiple zone and calculate each zone bill later, then you can utilize Zone Air System Sensible Heating Energy and Zone Air System Sensible Cooling Energy in order to calculate the percentage of energy use for each zone. Heating Coil NaturalGas Energy and Cooling Coil Electricity Energy need to be prorated according to the proportion of energy consumption in each zone because the model has only one heat source each for heating and cooling (Furnace for heating and DX Coil for cooling). For central HVAC system, energy fuels (Electricity and NaturalGas) are not consumed in zones, but consumed in the heat source. If you want to charge the consumed energy to each zone, the consumed energy needs to be prorated according to the proportion of energy distributed to each zone. If there are three zones (Zone A, B and C).

Zone A:Electricity Energy [J] = Cooling Coil Electricity Energy [J] × Zone A:Zone Air System Sensible Cooling Energy / (Zone A:Zone Air System Sensible Cooling Energy + Zone B:Zone Air System Sensible Cooling Energy + Zone C:Zone Air System Sensible Cooling Energy)

There is a similar issue in this question response by @keigo. https://unmethours.com/question/55005/hvac-energy-consumption/#55304

"if you want to model the multiple zone and calculate each zone bill later, then you can utilize Zone Air System Sensible Heating Energy and Zone Air System Sensible Cooling Energy in order to calculate the percentage of energy use for each zone. Heating Coil NaturalGas Energy and Cooling zone....Cooling Coil Electricity Energy need (Fan energy too?) needs to be prorated according to the proportion of energy consumption in each zone because the model has only one heat source each for heating and cooling (Furnace for heating and DX Coil for cooling). For central HVAC system, energy fuels (Electricity and NaturalGas) are not consumed in zones, but consumed in the heat source. If you want to charge the consumed energy to each zone, the consumed energy needs to be prorated according to the proportion of energy distributed to each zone. If there are three zones (Zone A, B and C).

Zone A:Electricity A:Cooling Electricity Energy [J] = Cooling Coil Electricity Energy [J] × Zone A:Zone Air System Sensible Cooling Energy / (Zone A:Zone Air System Sensible Cooling Energy + Zone B:Zone Air System Sensible Cooling Energy + Zone C:Zone Air System Sensible Cooling Energy)

There is a similar issue in this question response by @keigo. https://unmethours.com/question/55005/hvac-energy-consumption/#55304

"if you want to model the multiple zone and calculate each zone bill later, then you can utilize Zone Air System Sensible Heating Energy and Zone Air System Sensible Cooling Energy in order to calculate the percentage of energy use for each zone....Cooling Coil Electricity Energy (Fan energy too?) needs to be prorated according to the proportion of energy consumption in each zone because the model has only one heat source each for heating and cooling (Furnace for heating and DX Coil for cooling). For central HVAC system, energy fuels (Electricity and NaturalGas) are not consumed in zones, but consumed in the heat source. If you want to charge the consumed energy to each zone, the consumed energy needs to be prorated according to the proportion of energy distributed to each zone. If there are three zones (Zone A, B and C).

Zone A:Cooling Electricity Energy [J] = Cooling Coil Electricity Energy [J] × Zone A:Zone Air System Sensible Cooling Energy / (Zone A:Zone Air System Sensible Cooling Energy + Zone B:Zone Air System Sensible Cooling Energy + Zone C:Zone Air System Sensible Cooling Energy)"

This example is for three zones, but you could apply the same equation and extrapolate to 40 conditioned zones.

Are all 40 conditioned thermal zones in parallel on the supply side of the HVAC system? If not, this equation would not apply. This may not apply for the given HVAC system you are using. Can you post your node diagram?

There is a similar issue in this question response by @keigo. https://unmethours.com/question/55005/hvac-energy-consumption/#55304

"if you want to model the multiple zone and calculate each zone bill later, then you can utilize Zone Air System Sensible Heating Energy and Zone Air System Sensible Cooling Energy in order to calculate the percentage of energy use for each zone....Cooling Coil Electricity Energy (Fan energy too?) needs to be prorated according to the proportion of energy consumption in each zone because the model has only one heat source each for heating and cooling (Furnace for heating and DX Coil for cooling). For central HVAC system, energy fuels (Electricity and NaturalGas) are not consumed in zones, but consumed in the heat source. If you want to charge the consumed energy to each zone, the consumed energy needs to be prorated according to the proportion of energy distributed to each zone. If there are three zones (Zone A, B and C).

Zone A:Cooling Electricity Energy [J] = Cooling Coil Electricity Energy [J] × Zone A:Zone Air System Sensible Cooling Energy / (Zone A:Zone Air System Sensible Cooling Energy + Zone B:Zone Air System Sensible Cooling Energy + Zone C:Zone Air System Sensible Cooling Energy)"

This example is for three zones, but you could apply the same equation and extrapolate to 40 conditioned zones.

Are all 40 conditioned thermal zones in parallel on the supply side of the HVAC system? system, connected to the same demand side loop that is providing the conditioning equipment (coils, fan etc.)? If not, this equation would not apply. This may not apply for the given HVAC system you are using. Can you post your node diagram?