I think most people used plywood.
I used cedar planks, cut to size. Better water/moisture resistance IMO. But then the original plywood lasted decades...
None of my local hardware stores carried "marine grade" plywood. All they had was "exterior grade". They could get me the marine, but it was much more expensive. I don't think it was worth it, "exterior" would have been good enough.
Use only butyl tape to reseal the windows
Use stainless steel screws to put it back.
Make sure you clean the window flange and trailer before putting the window back on.
I used a metal brush on my drill to clean the grime off, then some "Scrubbing Bubbles" cleaner.
Don't over tighten the screws.
If you have a window crank that's not working right, it'll be the time to replace it, as the window must be off to fix it.
It's not a difficult job. The hardest part for me was to remove the old silicone sealant the previous owner used, and unglue the ensolite insulation from the wood frames. It's easier if you have someone to help when the time comes to take the window off or put it back in, especially the larger windows.
Lots of pictures on my renovation thread: Working on a Trillium 5500