It won't hurt anything but until the water is in the skimmer the skimmer isn't effective at cleaning debris off the water surface. How far above is it? Evaporation could take a while.
+1. And by vacuuming to waste, you won't have to clean your filter as soon after vacuuming. I have a sand filter, so I take the opportunity of too much water after a rain to backwash my filter thoroughly. Might as well get some good use out of having to dump water...
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