PokéBase - Pokémon Q&A
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Will this altered save data spreads like a virus to the other games compatible with Pokémon HOME and affects my games’ save file and my Nintendo Account? I’m just not sure if it will cause problems with transmissions because I don’t have the best judgement and i’m looking for the best answers especially experts here. :)

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What kind of altered save?
If you have an "altered" save file (I'm assuming hacked), then I suggest you don't use HOME with that save file because it could very well brick your Switch.
Like when I deposit a legit cloned Pokémon in Pokémon HOME.
It *should* be fine then.
It only happens when I deposit a God Egg, hacked/illegal Pokémon, but not pokemon with legal moves? Does this also affects my Nintendo Account since it’s linked to it?
The only way something could happen, is if you somehow created an intelligent virus inside your game that knows how to spread across your switch and access your account. If not though, mere broken code cannot effect your account. But in some cases, it can effect your console (soft-locks, crashes, or an unbootable system). Pokemon HOME doesn't really let you do anything "illegal," so I recommend that you don't use it if you're gonna be hacking.
Unless I set up Two-Step Verification? It won’t hack my Switch and my Nintendo Account?
2FA is always a good option for an extra layer of security (for your account only). But I doubt that anything could happen though just by hacking your game. If anything, it can only effect your system (depending on how big the hack is). All I can really say is: Know what you're doing, don't do any game/console breaking hacks, don't install custom firmware, and keep it simple/legit. And about altered pokemon, they can't become viruses, and they can't go into HOME. Stuff like hacked eggs, items and moves that just have "???" for a name, and pokemon with incomplete code can corrupt your save data (just for your pokemon game). Then you'll have to restart. But that's it.
Tbh, look, I don’t do any hacking on my Switch. I keep it simple and legit, i’m just being doubt about it’s legitimacy since I got it from someone else and I deposited it for the first time in a cloud storage like Pokémon HOME. Don’t know if this affects other save data (for Nintendo mobiles games) linked to my Nintendo Account
... :l, well you have nothing to worry about. It can't move around unless you move it manually. And it can't effect your account or games linked to it, because viruses are programs, and I'm pretty sure you can't write an entire program in a pokemon and get it to run in HOME. If you're in doubt just trust yourself and get rid of it, or put it back in the game you got it in.
So even if I release hacked pokemon, will hackers still find the data of a released pokemon?
I'm pretty sure that's impossible, once a Pokémon's released it's gone for good (in some cases it can be found in the wild). Unless the Pokémon was generated there's no way to have an exact replica of a released Pokémon.

1 Answer

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There is an option in Pokémon HOME where you can switch the save files around so for example, you could bring your Espeon that you caught in your original save, and transfer it to a different save. This option is above your saved games.

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