PokéBase - Pokémon Q&A
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Your pokemon faints.
Sub can't protect that, just like sub doesn't stop burn or posion.

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It does stop sleep, burn, poison or paralysis in the form of Hypnosis, Will-O-Wisp, Toxic, Poison Gas, or Thunder Wave.
Forgot Spore
I meant that when a sub is up, you're still burned or poisoned.
He means when you are burn or poisoned before you set up the sub you still take the damage