I think there's lots of good opinions that all could be why they "lose" a mold for sure.
Theft, poor archiving, destruction, etc., are all very plausible. I know from some experiences with injection molds overseas that factories do indeed have TONS of molds, sometimes anything from plastic utensils to model kits, in their factories, and they're easily misplaced.
Consider this... I live near an operating specialty steel mill... People walked out for years with TONS of stuff from the mills when I was growing up, and even with security tightened substantially, things still turn up missing... Mills like that and toy production factories in China aren't too dissimilar I'd wager.
I'm just playing devil's advocate... It sounds like Hasbro's trying to pick up the slack on those one way or the other, so I'm not too angry with them... yet.