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With central cooling or heating, there's only one thermostat and it is in the living space zone and not the basement, so the basement will almost always be colder or hotter than the setpoint. Which direction and how much depend on how the basement supply airflow, as determined under design conditions, compares to the load in any given hour.

There are assumptions in the model about heated basements, like the amount of passive air exchange with living space, internal gains, infiltration, etc., that likely affect the balance between over and under conditioning, but it is difficult to know what the balance should be and how to improve upon the assumptions.

With central cooling or heating, there's only one thermostat and it is in the living space zone and not the basement, so the basement will almost always be colder or hotter than the setpoint. Which direction and how much depend on how the basement supply airflow, as determined under design conditions, compares to the load in any given hour.

There are assumptions in the model about heated basements, like the amount of passive air exchange with living space, internal gains, infiltration, etc., that likely affect the balance between over and under conditioning, but it is difficult to know what the balance should be and how to improve upon the assumptions.

Edited to add: Note that we are in the process of transitioning ResStock to then OpenStudio-HPXML workflow, which uses only one conditioned zone (basements are not separate thermal zone). So this will no longer be an "issue" using that workflow.