The English rules (p. 2, left column) say:
On each Character card a particular Invention is depicted. The matching card should be removed from the Invention deck and put face up (Invention side up) on his or her Character card.
I say (and play) that the unused character-specific inventions go into the Invention deck. Interestingly enough, when Ignacy recorded his video of how to set up the game he actually removed the unused character-specific inventions from the Invention deck. I think that was a mistake, though.