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I know this is very old, but in case you're looking for a fix then here it is: You have to make sure that your reference body is exactly the same nif file as the one you built for your character body via the bodyslide. Just load a new reference from file by picking the corresponding body nif from ShapeData folder and make sure to tick the "merge new sliders with existing sliders" box. Doing that will reveal all the ingame clipping that is otherwise unseen. Also if you have several armor pieces equipped and there's still clipping make sure that each one of them has the same body reference.