If Naturalism is true, then many of Parfit’s claims are indeed wrong and his perspective is indeed askew. Does it follow that his efforts (and consequently much of his life) have been wasted? I do not think so. Almost all those who have engaged in any form of inquiry have been wrong and misguided...
But Parfit's concern is not that, if he's mistaken, then in virtue of being mistaken his philosophical work would have been a waste. Not at all. Rather, his worry is that if metaethical naturalism is true, then this would mean there are no substantive questions in normative ethics, and hence all his work in normative ethics would have been wasted -- not because it's mistaken, but because it was addressing empty questions. It would be a waste in much the same way that it would be a waste to dedicate your life to a merely verbal dispute: whether the pope is a "bachelor", say, or whether a tree falling in an empty forest makes a "sound".
Here's the relevant passage from On What Matters (vol 2, p.367):
Naturalists believe both that all facts are natural facts, and that normative claims are intended to state facts. We should expect that, on this view, we don't need to make irreducibly normative claims. If Naturalism were true, there would be no facts that only such claims could state.
If there were no such facts, and we didn't need to make such claims, Sidgwick, Ross, I, and many others [i.e. normative theorists] would have wasted much of our lives. We have asked what matters, which acts are right or wrong, and what we have reasons to want, and to do. If Naturalism were true, there would be no point in trying to answer such questions.
As is clear from this passage, it isn't mere falsity that renders one's philosophical work a "waste". There are two clear indicators of this. (1) Otherwise, he would already think that at least one of Sidgwick and Ross, in virtue of advocating conflicting theories, must have wasted their lives. And he certainly doesn't think that! (2) Naturalism is a metaethical view that Parfit argues against. But he isn't concerned that if he's wrong about this, it renders his metaethical work a waste. Rather, it's the value of his normative work that is under threat -- and at no point does he worry that his normative views are false. The worry is instead that the questions are empty -- that there is "no point" in answering them.
It shouldn't be controversial that some philosophical projects are a waste of time -- and getting bogged down in a merely verbal dispute, or addressing otherwise "empty" questions, is surely the paradigm of such "wasted time".
What's more controversial, of course, is Parfit's claim that normative ethics can only be substantive if metaethical non-naturalism is true. Reasonable people can disagree about this. But it's hardly a surprising view for a non-naturalist to take, since the main motivation for non-naturalism is precisely the sense that it's the only way to take normativity seriously, i.e. to secure a domain or subject matter for normative ethics to be about.
I've similarly argued that questions about what entities are conscious (what we might call "first-order" philosophy of mind, by analogy to first-order ethics) can only be substantive if dualism is true. If physicalism is the true theory of "meta-mind", then once we know all about the physical functioning of my silicon-chip duplicate, there's nothing left to know about whether he's "conscious" or not. There's no further question there. So someone who dedicated their life to answering that (non-)question would be, naturally enough, wasting their time.