There are a variety of cards or abilities that interact with prepped spells. There are also several spells that can self destruct as part of their cast effect. If a spell is destroyed, it is removed from the game, and any further effects that target that spell cannot be resolved.
Example: Kadir has Conjure the Lost prepped (Cast: Deal 5 damage. You may destroy this. If you do, Gravehold gains 4 life.). She casts it using Vortex Gauntlet (Cast any player's prepped spell. Return that spell to that player's hand.), and chooses to destroy the spell to heal Gravehold. Since the spell was destroyed, it is not returned to her hand.