In reference to Boni's comment I have seen a .cr2/pz3 reference 2 pmds somehow mysteriously with no explanation, and no means of determining the cause with a utility called Binary Morph Editor that let's you view and edit the contents of pmd files. At least that's what APPEARED to be happening. It occured during many many file saves of a character loaded with probably a hundred or so custom morphs. IIRC it sort of resolved itself during a subsequent save. I can see if something like that were to happen and you were to delete a file during the midst you could lose some morphs...