To clear things up, I think he's saying that just because an argument is a fallacy, that in and of itself does not automatically make the point being argued wrong.
Yes, I agree. In fact, that's the aptly-named Fallacy Fallacy.
Well, my argument is wrong, but the sky IS indeed blue.
Of course. The problem comes from the burden of proof. If a claimant has it, and supports it with a fallacious argument, the claim fails. That specific claim fails, to be sure. But if the claimant still wishes to propose his statement, he has to find another argument for it or withdraw it. Where a presumption is appropriate, the presumption will continue to hold upon failure of the alternative argument.
Using your example, if you wanted to argue that the sky on some other planet (i.e., such that it can't be observed directly) were blue, and your argument in support of it were undisputed evidence that the atmosphere contained water, your argument would still fail. But that failure doesn't affect whether the sky really is blue. It doesn't prove that the sky is not blue. Nor does it mean that some other perfectly valid argument can't be made in favor of your same proposition.
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