I've never done it, but I'd expect if you leave it zipped in it'll crease pretty badly.
But there are other options. One is to unzip it, but leave the bar mounted in place so the window simply flops down into the rear cargo area. The other option is to unzip only the sides of the window, unsecure the bar, and roll the window up. The rolled window can be secured by the two elastic straps that should be dangling from the interior of the soft top.
The second option is "technically" the correct one, though it will scratch the window over time.