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They don’t ban you just for having modified software, they will usually ban you for pirating or cheating. It’s reasonably safe to go online with homebrew if you aren’t pirating or cheating but there’s no guarantee, they could still ban you at any time for anything

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All it takes is to connect to the store or multiplayer gaming services with the customized O/S and you might be a lucky candidate to have your device banned. From all accounts this doesn't appear to be an automated process, or happens rather randomly.

I agree that those who sideload pirated games and then take those games online are most at risk to have their device bricked.

You could be, but I don’t think there’s any evidence of that ever happening with the Nintendo Switch specifically

It’s hard to be sure because not everyone who pirates or cheats will admit to it and there’s a lot of conflicting information online but I go online with Atmosphere booted sometimes and I’ve never had any issues and many others do the same

I don’t think Nintendo have any way to know if all you’re doing is booting a custom OS unless there’s detection code that no one found yet

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