I've never thought that anything would be deleted. Even if the super dragonballs would restore the universes, there's nothing to stop Zeno from deleting them all over again as well as the offending universe who made the wish. My guess is the threat of deletion was simply to produce the best possible fighting tournament after seeing Hit vs Goku and that the Zenos had no intention of deleting the universes. This could lead into the Grand Priest being all ominous.