Unless you are blending different exposures to capture objects of extremely high dynamic range (M42 is the prime example), you shouldn't be mixing ISO settings. You will get the best results, and have the simplest pre-processing workflow, if you stick to whatever ISO setting gives you ideal results with your scope and skies. ISO is just a change to gain, which affects FWC (saturation, to be more exact) and read noise. This affects dynamic range, however if you are using the proper exposures, you should be making ideal use of the DR you have anyway. Some slight clipping of the brightest stars is usually a preferable tradeoff for getting the lower noise that a higher gain offers. If you can do that at ISO 1600 and not be stuck with exposures that are just too darn short, then use ISO 1600 for everything all the time, and don't bother changing your ISO at all.
Even in the event that you do end up imaging a very high dynamic range object like M42, the better solution to handling it is to reduce your exposure, but otherwise keep all the other settings, including ISO, the same. You can halve your exposure to get the core of M42, and blend it into the rest of the longer exposure data for the fainter outer details. If you do things right, you could reuse both bias and flat frames for both (since ISO did not change), and you would only have to get different sets of darks for each set of exposures.