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>"Fainted" Pokemon aren't literally injured or unconscious. In the Japanese games, it's explained that "fainting" or "near death" as it's called in Japanese, is a hyperbole, and just means that the Pokemon is too tired to continue battling, which is why they can still use HM moves in the field, and when viewed in Pokemon-Amie, are seen simply taking a nap. Pokemon hold back when they battle, and never fight hard enough to risk any major injury.
