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It sounds like you are trying to accomplish something similar to return air integrated into lighting systems. In those systems, the conductive heat from the lights is captured by the return airstream, and does not enter the space. With your window system, you will be doing the same thing. The major difference is that by using the cavity between the two panes of glass, you are eliminating the insulating properties of this air gap. If you would otherwise use single pane glass, then you might see some energy benefits.
In regards to how to model it - you can use EnergyPlus's "airflow windows" to model airflow. See the example file AirflowWindowsAndBetweenGlassShades.idf