Is it rotted above the window as well? If so then it was your roof leaking. I'm doing the same repair right now and had to remove the fiberglass on the outside. Mine was rotted down to the lower sill of the wall. Since i'm doing the roof and all it was easier to go this route for me. The outer skin of the outside plywood will stay stuck to the fiberglass. Need more outside pics of yours to assess the scale of the delamination.
The window was originally installed with butyl tape under the lip of the flange. You could either do that or get some good quality window sealant at the box store. I'd finish it off with RV sealant on the outer edge of the frame.
