We've had ours 13 months now so that's not enough for a long-term answer about the windows. For that matter the hardsides are so new (from FR at least) that theres no way to tell about long-term sun damage. So far there's no evident damage from the sun and we don't cover ours in the summer. I'd be more concerned about a cover scuffing the window when there's a wind. Some covers have a soft lining in strategic spots to avoid that.
You might try looking at Aliner/Chalet owner forums to see if anyone there has had problems like we're talking about. Those units have been around for years.
It's never too late to have a happy childhood!
Lee, WU0V, and Courtenay, N0ZDT
2011 Rockwood A128
2000 Silverado 1500 pickup
60W solar system
2000W inverter generator