You don't need to clear the polygons to do alpha sorting. You just need to swap which particles use which vertices. But then you have to reset the alpha, color, etc, even if they haven't changed for a particular particle. But I'm not sure there's even really a speed hit associated with that. And I'm not convinced there is a speed hit for clearing the polyogns from a mesh either. Blitz seems to update the whole mesh regardless of whetehr you change one vertex or all of them, so there may be no speed hit at all from clearing the polygons.
Single surface question
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