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Already fixed in the latest commits Gen 6+ have the ability capsule which allows ability changing, which is why the message didn't appear on recent generation saves.

Save files for the 6th and 7th generation are always called main by default and have the following sizes (no matter if it's a real 3DS or Citra): XY - 405 KB (415,232 bytes) ORAS - 472 KB (483,328 bytes) SM - 431 KB (441,856 bytes) USUM - 435 KB (445,440 bytes) Anything else is not a save file! If your file matches the correct size and PKHeX doesn't recognize it though, there must be something wrong with the data in your file. If you upload your save file someone could check what might be wrong. By the way the best solution for any issues with citra is transfering your save file onto your 3DS. Also I would recommend to use an official build of citra https://citra-emu.org/download/, the Photo Club issue is fixed in the latest Canary builds and speed was improved as well (though there's still issues on AMD and Intel GPUs). @Rfoxes If you have selected your game directory in citra (in the file menu) you can right click your game in citra's main window to open your save data location.