on a Trillium
use rubber seals in the construction of the window, but the window is installed using butyl tape, not rubber. To remove the windows, pull off the plastic screw covers, remove the screws, they may be quite rusted. Pull the windows out from the bottom. They kind of hook in at the top. Clean the old butyl tape off both the windows, and the shell of the trailer. Inspect the wood that he the windows screw into. If it is dry and solid, then leave it. If wet and rotten, then carefully peel the ensolite away from the wood. Try to not damage the black ensolite foam. I have found it much easier to remove rotten wood then wood that is in good shape.
New butyl tape is available at the parts department of your local RV dealer. Line the flange on the window with new tape. Reinstall the window, top first. Use new screws. I would use stainless screws and nylon washers to limit corrosion as the result dissimilar metals.