I don't think Sculpey will do anything bad to the mold. Your biggest problems will be having the mold deform while you're pushing the sculpey into it, and having the piece deform while you're pulling it out (Don't put the mold in the oven to harden the Sculpey)

You might try casting the mold with plaster and only demolding the one piece you want. By leaving the other pieces filled, the mold will probably be stiffer when you're pushing in the sculpey.

Steve