I don’t see how they can be in that folder, and appear in search results as in that folder, but not be visible when you go and look in the folder.

How many files are we talking about here? I take it from your trench/spoon analogy that there’s quite a few of them?

You can mbum-select from search results, so if that really is the only way you can get them to show up you could copy the font files out of the folder, delete everything out of the folder via the search page (using a fairly generic search that’ll match them all), then move the fonts back.