open your sd card with a file explorer and then proceed along this path:
private>wii>app>rsbe>pf>stage>melee
This folder called melee holds stages used in vs mode. To restore a default brawl stage, you must simply delete the one that "goes over" it. For example, P:M final destination is labelled STGFINAL.pac. Delete this file, and you will now have the vanilla brawl final destination.
This is where is gets complicated. Several years ago, Brawl modding advanced to the point where it was possible to place a stage such as final destination over another stage, such as Big Blue. This requires that one rename a final destination stage as STGDXBIGBLUE (dx tells you that the stage goes over/is one of the past melee stages), and supply a "rel" file. Rel files are found in the module folder. If you want to restore bridge of Eldin for example, you need to delete both STGOLDIN in the melee folder, and st_oldin in the module folder.
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I will be updating my stage thread as soon as I complete my newest one.