when we say that "messing with the brain messes with consciousness", how do we really know that?

Everything about someone's personality and mental functioning can be affected by affecting the brain. Take an example; people with a certain type of brain damage can stop recognising faces. Their qualia have been fundamentally messed up. They can see the world just fine, but if their mother comes to talk to them, until she says 'hello' and they recognises her voice, they don't know who she is.

There are so many cases like that.

Now do you really think that it's fifty fifty on whether their consciousness has been affected by the brain damage? I mean, what's the alternative? That they're recognising their mother and choosing not to act on it? That their consciousness has disassociated with action, and inside their head they're thinking 'Help me! Help me!' whilst their body says "I'm sorry, I don't recognise you"?

All the components of your mind are created by the different modules in your brain. When you affect the brain, it totally messes up your mind. When the brain stops, the totally best guess is that consciousness stops too.