PokéBase - Pokémon Q&A
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I want to perform a system transfer, but my 3DS states my Ultra Sun software will be deleted on the receiving system. Will I lose the entire game save if I go through with the transfer? If not, what parts will be lost?

I don't think this breaks the rules about hardware because it specifically relates to a Pokemon game.

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Pretty sure for any game you have on a cartridge, the only thing that's stored in the system is any updates.
So if the receiving system deletes data, the only things that are lost are the patches/updates? Will they have to be redownloaded when I attempt to play again?
Yes, you'll have to redownload the update to access online features. I placed Pokemon X in a new 3DS I have. My progress is still on the 3Ds and I just had to redownload the update.
Are you playing on a cartridge?
I'm playing on a cartridge and the system in question is a New Nintendo 3DS XL.
If you do a system transfer, you don't have to worry about cartridge save data being deleted, as save data is stored on the cartridge.
I’m too lazy to read the thread right now, but if it helps, I have multiple 3DS’s and I’ve never had an issue playing my games on any of them. My saves function normally on all the 3DS systems, despite them all having different update versions of the game. The save file is 100% on the cartridge and the save should not be deleted.
they’re probably just deleting the “title” to prevent any corruption issues. It would probably cause some issue if there were two versions of the game on the ds.
Can’t really answer what exactly will be deleted, but I can place my bets it’s just the title and update data

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Best answer

The only thing saved on your system that would be lost are updates/patches.

The cartridge itself contains your saved data, and thus it shouldn't be lost if you're using one.

That said, the save data could be lost if you're not carefully following the procedure below. Make sure you are especially careful with the SD card, as the 3DS has a very inconvenient formatting method.

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Thanks much.