When the PO skinned over the removed window openings on our Eagle, he did not remove the other ones that were left in. If it were me I would remove all of them, skin what you want, cut out the holes for the remainder and be done with it. I'm not sure how I will fix mine yet when I install the new windows that are in the process of a cross county journey. Use aluminum to re skin, ours is cold rolled steel and it has rust issues. Do it right the first time, otherwise two things, you won't be happy and you know what that means! It just won't look good. The less seams you have the less chance for leakage in the future, don't ask me how I know this!