PokéBase - Pokémon Q&A
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So let's say I try fighting a Pokemon, but my team won't survive against it so I run away until it stops chasing me. If I try to catch it outside of battle, will it still treat the catch rate with the HP in mind?

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No, it won’t work. If you run from a battle, the Pokemon is still "targeting" you (the red eye at the top of the screen). In this state you can’t throw balls at them. You can go back into battle though, and they still have low HP.

However, if you run far away enough that they stop targeting you, their HP gets restored. So throwing balls at them will not have an increased catch rate.

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Huh, I could've sworn HP carried over, but I just rechecked and it indeed doesn't.