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Every Zero Isle resets your level to 1 in EOT except for the Northern one. Just wondering if it sets my Scizor's Protein boosts so it never happened (Scizor is apparently a Special Attacker in Mystery Dungeon -_- .)

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However, the player must start at Level 1 (both moves and statistics) and can only bring 16 items with them. The player's level and stats will be restored once they leave the dungeon and will retain any items found within.

Yeah everything is reset once you enter Zero Isle. However they are restored once you leave

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That doesn't say anything about my Vitamin boosts going  away necessarily...