To compensate for the thermal radiation loss that an IR window will cause, you need to enter the transmission value of this window into the camera.
The GenICam registers "ExtOpticsTransmission" and "ExtOpticsTemperature" need to be updated in the camera. These can be found under the GenICam header "ObjectParameters." The GenICam register "EstimatedTransmission" needs to use the calculated value—if you set it to something other than 0, the camera will not use the calculated transmission value.