Can you fight moltres again if you kill it in Pokemon HeartGold?

Yes, you will be able to encounter Moltres again provided you have defeated it but this only applies to Pokémon Platinum, Pokémon HeartGold and Pokémon SoulSilver. You have to defeat the Champion in order to respawn a fainted Moltres.

This will not work in games such as Pokémon Red, Pokémon Blue, Pokémon Yellow, Pokémon FireRed and LeafGreen.