The only way to fix a window that's had a BB shot through it is to physically replace the window pane. But there is a way to cover up the hole in the window. According to the Popular Mechanics book "When Duct Tape Just Isn't Enough," all it takes to fix is a bit of nail polish and some patience.
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Apply a small amount of clear nail polish over the top of where the BB hole has pierced the window pane.
Fill the BB hole completely with a solid layer of nail polish.
Allow the nail polish to fully dry.
Apply another coat of clear nail polish into the BB hole. This layer will accumulate on top of the first layer of clear nail polish, and begin to fill in the hole.
Allow the nail polish to completely dry, then repeat this process until the layer of clear nail polish lines up flush with the window pane.