Will we lose that reservation if we're not onboard in Freiburg?
No, travel documents are valid for the entire route printed in the ticket/reservation, so it doesn't matter whether you intend to use it for the whole route or only some parts of it, you've payed for the whole route. So we don't see any problem boarding CNL 459 in Karlsruhe instead of Freiburg. And if you
email CNL directly, they should confirm it.