Meta Battle Subway PokeBase - Pokemon Q&A
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The next time you encounter it, it will have full HP.

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when can you battle it again?
If it is not a roaming Latias, when you defeat the Pokemon League. If it's a roaming one, you will encounter it again in tall grass if the Route it is in matches your own. If you and Latias were in Route 1, for example, you'd find it in the tall grass on Route 1.