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[[File:Pokémon Shuffle logo.png|thumb|Pokémon Shuffle logo]]
Two patches for Pokémon Shuffle have been released in quick succession. They must both be downloaded to obtain check in bonuses.
The first patch is a major patch that updates the game to v1.1.0, and is downloaded from the eShop (although the player will be prompted to go to the eShop when attempting to check in on an older version). After installing this patch, the player will lose access to Special Stages.