It depends upon the the thickness and quality of material that was used when it was installed. The old factory top would flop right into place but it was 27 years old and torn by then. The new top has been taken care of but shows a little bit of age there and there. It is still difficult to get it stretched closed and then the clamps must be fully extended form them to grab the notch. I did the same as you and had left the top down for quite some time with the boot attached. The plastic window developed a crease in one area that took some time to come out but now it is not visible.

Bjorn said that he used to place a soft terri cloth towel in the fold of the top when lowering it but I have not yet down this.