Many owners have used covers for years and have no issues with the windows. Maybe the big 400 stargazer window might be a concern, but there have been no reports of anything like that happening. My cover is securely fastened to the trailer with the installed straps on the cover. I use spring clamps around the edges to prevent any movement.
If anything the cover will abrade the plastic trim along the sides and to some degree the back before it scratches the windows. My trim was slightly hazed with one winter of not covering them. The most vulnerable windows are the stargazer and front window as the cover tends to rest and rub against these. With that said I try and cover ALL of the windows and trim with plastic cling wrap (the stuff they use to wrap palettes) but Saran Wrap as well.
Covering the windows will help with some scratching from the cover but still plan on polishing the windows every year or other year. They will still get some minor scratching from general use and may get a bit cloudy over time. Ours did. Maybe oxidation? I polished ours this past summer for the first time and they looked almost brand new. I will still cover them when the trailer is under its cover for the winter and will plan on polishing them every spring.
We live in Fl and whenever we put our 400 in storage, we use a cover and have since purchasing in 2019. We have custom wrap on both sides and the trailer looks as good as the day we purchased it. No issues with the windows.
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