Thanks for the manual on the instrumentation; I learned something new! The sensor you called a thermocouple is actually a heat flux sensor with an integral thermocouple. I didn't know about that before, now I understand how you get heat flux, it is measured directly.
I made the following figure to represent your Thermal Wall. You have a cold side where the bulk temperature of the air is Tbc, you have a heat flux sensor on the glass measuring the glass temperature on the cold side of Tgc and the heat flux qgc. You have a hot side where the bulk temperature of the air is Tbh, you have a heat flux sensor on the glass measuring the glass temperature on the hot side of Tgh and the heat flux qgh.
Outside of the controlled temperature environments on either side of the wall is the lab space where the temperature is Tlab and that is where the voltages are being measured, probably on the FluxTeq DAQ. Is the correct?
My point on a previous post was that the temperature of the glass on the hot side could be very different near the top where there is a trapped wedge of air next to the glass than it is near the bottom where there is natural convection occurring in the wall cavity.
That is why a better BC for your Thermal Wall model would be Convection on both glass surfaces. I assume you have some idea of the bulk temperature of the air on each side. But the issue is what is an accurate estimate of the convective heat transfer coefficient, h, for use in the CFD model convective BC?
Get two or three more thermocouples and plug them into the DAQ to measure the bulk temperatures directly. Also, it is more accurate to have a thermocouple measuring the temperature in the lab. Here is the updated figure.
Given that you have an actual heat flux sensor, you can calculate the convective heat transfer coefficient from the equation
h = q/(Tg - Tb)
which is the definition of that quantity.
Do this for the hot and the cold side of the wall and use each value of h in your convective BC along with the measured bulk temperature.
Finally, looking at the photograph of the Thermal Wall, I see a wooden frame on the sides and top and bottom of your Thermal Wall, so I would make those four sides Adiabatic.
There is a lot more detail in the heat flux sensor manual you provided above. Are you implementing the temperature correction for the heat flux? I assume you read the bit about the voltage output from the thermocouple gives you the temperature difference between Tg and Tlab so that if you want the absolute value of the temperature of the glass, Tg, you have to add Tlab to the reading from the thermocouple. How are you measuring Tlab? You could do that with an extra thermocouple.