If that is just with water, you may be in trouble when you start growing the yeast. The liquid may become viscous enough for the fan to run out of grunt and stop (I have had this happen with a 60 mm stir bar in 3L starter).
But AFAIK, as long as the yeast is being agitated, you don't need a big *** whirlpool.
Might throw the stirbar into a whammy but i don't think you would stop the fan, maybe disengage the magnetic drive is about all. Besides, you only want the stirplate running to aerate the wort for good yeast growth, then turn it off, don't aerate the fermenting beer and risk oxidation if you want to pitch a nice clean starter. I turn the stirplate off as soon as there is a good krausen formed, fermentation keeps going and finishes out all by itself, thats when I refrigerate.