One thing I noticed that when taking exposure, 16803 fan becomes much quiet (I assume because fan speed is reduced). If this is true, does it mean that cooling efficiency will go down? Eg, if I cool CCD to -20C with 80% cooling (fan would be fairly noisy at 80%), what would happen during long exposure? 16200 does not seem to reduce fan speed automatically during exposure.
Take a short image, do a long image, compare the temperatures of the CCD sensor in the FITS header of both images.
The fan speed should adjust automatically depending on the heat sink temperature. It shouldn't care whether an exposure is in progress or not.
The most important thing is to check whether the CCD temperature is remaining stable during the exposure. Also watch the power LEDs on the side of the camera. Is the voltage remaining stable?