I would say a factory unmolested windowless body is worth more due to desirability and want.
One with filled in windows still has the windowless desirability but probably not worth more then a windowed version.
A lot will have to do with the quality of the fill. I see so many with obvious shrink backs in the paint, cracks in bog etc.
It can be done correctly with complete side panel replacement but the cost to do this will most likely exceed any increase in value.
I'd say you'd be better off leaving it alone.
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