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Deleting the surfaces in Pic 1 is no ta good idea and can produce unpredictable results for the floor area and volume. I would suggest instead of deleting the surfaces between the spaces to use an air wall construction, and to make sure both spaces are assigned to the same EnergyPlus thermal zone. OpenStudio should not include the floor area of the mid-atrium air wall in calculating internal loads per floor area, and OpenStudio will form a zone that looks very similar to picture 2.

Neither of these approaches (if you use advice for spaces in same zone) address vertical temperature stratification within the double height space.