In a post on Twitter, Nintendo of Japan has issued a statement saying it is aware of an issue plaguing the NSO GameCube version of Pokémon XD: Gale of Darkness that is wiping players’ save data. As is typical with posts like this, Nintendo writes, “We are currently investigating the matter to find a solution.” There is probably something going on with how the emulator creates save data on a virtual memory card, if I had to guess.

For the moment, Nintendo suggests using the GameCube app’s built-in save states to back up your progress. While that is a temporary fix, it does at least give you some confidence in turning off Gale of Darkness without worrying if you’ll need to repeat hours of gameplay. On Reddit, a number of users have claimed they lost ten or more hours thanks to this bug, so I would definitely start making quicksaves.
While problems like this don’t crop up too often for Nintendo’s official emulators, there have been instances with game breaking bugs in the past. When Kirby 64: The Crystal Shards was added to the N64 app, there was a game breaking bug that would freeze Kirby in place if you took damage underwater. There have also been general graphical glitches in a lot of N64 games, which is a notoriously difficult to emulate console.
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