I always chop the top, I see no reason to unnecessarily add extra stress to the plastic window. I also recommend you avoid putting the top up or down below 70° F, unless the car has been in the sun and the plastic is flexible. If it's a real issue, you can always retrofit a glass window onto older style top frames, but the rear window will be narrower.
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1999 Ocean Blue Metallic Boxster - blueboxster.com
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