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Why would they have been wiped out across the entire continent, other than in the isolated pine barrens, swamps and barrier islands of NC, SC, GA and northern FL, though?

I don't know, but one possibility is that the Carolina Dogs represent the oldest canine population, in terms of residence on this continent. If immigration from Northeast Asia was continuous over several thousand years, later arrivals might have brought different breeds which either overwhelmed and assimilated any Carolina like canines elsewhere in what would become the U.S. and Canada. If the Bering Strait "bridge" during the Ice Age theory is correct, then the coastal Southeast would represent the opposite end of the continent from Alaska. Newer migrants, dog and human alike, may not have penetrated these areas in the pre-Columban era.