You might be able to make the missing windows using PVA, although the openings might be just a tad too large for it to work.
Using a cocktail stick or similar, spread the PVA around the edges of the opening, and move across until it fills the window. Leave to dry, and it should form a clear 'skin'.
It works on opening up to about 1/4 inch - any larger, and it'll either still form a clear film, but have a depression in the center, or it'll just form part of the 'window' around the edges, with a hole in the middle !
If it doesn't work, the the 'film' can easily be peeled off, leaving a clean opening. Windows without glazing may look better than glazing with frosty glue marks.