Well, the folder structure was actually still setup exactly the way it had been, he just didn't see it inside of any of the apps he was using. I offered to show him how to use his folder method if he would just try my (read MacOS's) method of doing it. All the files were already tagged via ID3 or some other metadata as they were either MP3, OGG, or FLAC files.

His big realization was that he didn't actually care about how the files were organized so long as he could find the sounds he was looking for. He cared before because there wasn't any way to efficiently search for them by any meaningful method (finding "metallic" sounding effects, for example) and so he filed things away in folders so that he would only have to browse through a subsection of folders (in that case - materials->metals->metallic). Now he just searches the library for "metallic" and all the sounds come up and he can combine search terms for "loud metallic" or "warped metallic" or "wobbly metallic" and get exactly the sounds he's looking for.