Welcome to TFP...just my opinion, but if the cover is still in good shape and the water level is OK, the situation under that cover won't get any worse over the winter.
It likely turned to pea soup over the summer if there has been no circulation or FC added, but once water temps drop below 60 deg, it shouldn't get worse.
Well, you would be facing the same task now, just to cover it up again. My point is most of the damage is done, but if you prefer to clean it up now, I would suggest reading through pool school, specifically
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