Keep Safe can target a spell that has multiple targets, as long as at least one of those targets is a permanent you control.

A spell that can’t be countered is a legal target for Keep Safe. That spell won’t be countered when Keep Safe resolves, but you’ll still draw a card.

If the permanent you control targeted by the target spell leaves the battlefield, that spell is no longer a legal target for Keep Safe. On the other hand, if that target permanent becomes an illegal target for the target spell but remains on the battlefield under your control, the target spell is still a legal target for Keep Safe.