Two percent is what would be expected, since we ar...

Two percent is what would be expected, since we are talking about an affinity between a very small minority population in South Asia and a large population in Australia.

Not a large population in Australia. The lineages are always minor in Australia. Australia's C is mostly C4, which does not exist today anywhere else.

By all accounts the closest relatives of Australians by "wholesome" (autosomal or autosomal+haploid) DNA are Papuans and Melanesians. However their relation does not seem much more recent or intense than what they have with other Eurasian peoples separately, hence refers to the early colonization period basically, maybe slightly reinforced by their neighborhood.

Has a refutation been published? Is the new data incompatible in some way with that presented in 2002?.

I don't think Cordaux is making claims that would require refutation. This study was part of the process of understanding Eurasian mtDNA beyond the over-studied European and Native American cases. In 2002 the phylogeny of M and most of N was still a huge mystery (and would be for some years after that, even today researchers are still discovering new rare M sublineages and possibly N ones too).

Cordaux data though has to be read on the light of what we know now, almost 8 years later. And that's what I did when I said that his suggestion that South Asian and Australian mtDNA is different is perfectly consistent with our knowledge of India being strongly dominated by M and Australia by N.

They are aware of this and if you read the paper you'll see that they took such a possibility into account -- and saw only a South Asiatic-Australian connection for the particular haplogroup under consideration.

Again mtDNA N. There's no other link.

They see the connection as recent, ca 5,000 years ago, and associate it with the introduction of the Dingo, plus several other indicators of significant change in Australia during the Holocene.

It's a possibility but the relevant lineage is extremely minor at both sides of the Indian Ocean: it does not "magically" make both peoples more akin, just shows that there was (maybe - not sure if this has been sufficiently confirmed) a contact.