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Yes, air walls are a solution. Set both the constructions of the co-planer surfaces to the "Air Wall" construction. The two surfaces must belong to different spaces in different thermal zones. You'll need to also add the zone mixing object in order for it to work. There is a measure on the BCL called "air_wall_zone_mixing" that you can apply using "Apply Measures Now".

That aside, my opinion is that I don't think it's going to be a very accurate representation for vertical heat transfer depending on your ceiling heights. Stratification and natural convection aren't accounted for by default in E+ and thermal zones are assumed to be well mixed. Your model with air walls is really only going to give you the ability to share the load with both air volumes, rather than provide you with accurate zone temperatures. If that makes any sense...Look into the room air model if you want to try and predict zone temperature better for stacked thermal zones that share air.

Hope that helps.