PokéBase - Pokémon Q&A
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I have some competitive Pokemon with max friendship Return, I've heard that it's a false rumour that storing a Pokemon in the PC reduces it's friendship, so can anyone clarify that storing Pokemon does not affect friendship? Also does fainting etc in wifi battles or Battle maison reduce friendship or is that only ingame battles?

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No, storing a Pokemon in the PC does not lower its friendship. You can only carry 6 around at any given time and Gamefreak aren't that sadistic.

Fainting in wifi & battle maison (or other variants) does not affect friendship. Notice how your Pokemon don't turn towards you like they do in in-game battles (if you've bonded with them really well in amie).

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Cheers man
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In Pokemon Yellow, if you store your starter Pikachu in a box, you will lose 3 friendship points at friendship level 0-199 and 5 at 200-255. If your starter Pikachu faints in link battles, it loses 1 friendship point if the opponent is less than 30 levels higher, 5 at friendship levels 0-199 if opponent is at least 30 levels higher(including outside of battle),and 10 at friendship level 200-255. This only accounts for the starter Pikachu. The other answer is correct, I just wanted to add this.
Source: https://bulbapedia.bulbagarden.net/wiki/Friendship

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