In the logic of One Piece, as long as Lilith will live, Vegapunk won't die. Remember, Lilith is connected to Vegapunk's entire memory system. Which means that she knows everything he knew.
Think about it like a doctor Who transformation. Vegapunk is not in the same body and has different manners, but Vegapunk is still vegapunk.
So Vegapunk might leave the island alive.