Changes from Pokémon Diamond and Pearl
If the player defeats or flees from a stationary Legendary or Mythical Pokémon, it reappears after the player next enters the Hall of Fame. If the player defeats a roaming Pokémon, it will reappear only after the player has re-triggered the event which caused it to start roaming; for example, the player must talk to Professor Oak to cause a Legendary bird to resume roaming.
Emerald is older than DP, so it won't respawn if you saved after defeating Latios. (unless you delete your save)