NOT recommended! The plastic windows will crease and scratch. Better safe than sorry. If you want to carry your windows with you, I suggest you look into a window roll. There are a couple of companies that make them including Bestop and cloverpatch.
Take the windows out. If you want to see what will happen, check out rental jeeps in places like Hawaii (awesome research project! Let's all go!). I rented a Wrangler in San Diego - all five or six on the lot had beat-to-hell windows, because renters dont know/don't care.
Yes you have to take the windows out. The top will fold and tuck in so much better that way anyway. I don't like rolling up the windows, if it gets cool out and you go to put the windows back on and they're all curled up, that's no fun.
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