There shouldn't be any harm in "temporarily" storing it with the top down. But, if you choose that route throw a cover over the car or the interior to keep out the dust and such.
Personally, I always throw the top up at home or if it's sitting outside for any length of time.
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'06 Cayenne Turbo S, Beige Metallic/Tan
Ex - '99 Arctic Silver, Red Interior, Silver Top
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