A user somehow managed to rename an existing folder, and use a forward slash "/" in the new name. This caused error message(s), but somehow the folder was renamed. The new folder name did not have the slash in it, but it also was missing many of the files that used to be in the folder.
Looking in the database, those files were still there, and were still listed as being under the old folder name.
Some research turned up this Microsoft KB article
The fix was fairly easy - simply recreate the original folder, and all of the missing files appeared under this new folder.
I'm not sure how they managed to cause this problem. Doing my own tests I've been unable to recreate it.