Most were probably recycled...a couple of "probable" prototypes of the School time ponies have shown up in the past as well as a Starlight Baby.
More often than not prototypes like this are stored for a very short period and then destroyed - mainly so there is no risk of competitors actually getting a hold of them plus often for FMCG products companies dont think the items will have any interest or value in the future and churn through so many items that there is little point in them being stored. The fact that we as a collecting community seem to know more about G1 MLP than Hasbro is an indication of their lack of information retention!
Oh... that's a real bummer then.
I heard of the old molds being destroyed/recycled, but I didn't know that ponies met the same fate...
Well, joke's on them, since quite a lot of molds managed to be stolen away from Hasbro factories, anyway (as seen on the examples such as Princess "Rinse n' Spit" or Totsy ponies). But I can understand their concerns...
It's still a pity, though.
That Starlight baby looks similar to that Shy pose!Bubbles prototype, in that they're both ceramic figures. Cool.
Wonder how she ended up with the folks before Lancer...