The layout of your gut is unchanged, only the width of your stomach is smaller.
That means that the amount you can eat is restricted, but absorption is not. If your intake is high in fats, than can be absorbed quicker the with a normal stomach, and shoot your cholesterol level higher.
With RNY, part of the section where enzymes that break down fat for absorbtion is removed from the direct route, so, fat absorbtion is delayed and decreased, which makes it easier for the cholesterol level to come down.
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