Clean Audio Folder is something everybody tries once and then gives up on.
It was designed in the Win3.1 days when there was no recycling bin yet.
It had a bugfix in Newburyport, but the concept has never been updated.
The generally accepted workaround - GAW(R) - is to use "Save As", ensure you have "Copy All Audio with Project" selected, then save to a new directory.
You now have a new directory containing only those audio files you really use.
Unfortunately you now need to delete (or better rename) your original directory, then name your new directory to the original name.