I think they all are now updated; my understanding was that the chart for Doubtful Sound in New Zealand's South Island was the very last of Cook' s charts to be checked/updated, sometime in the mid 1990s. That said, those updates are perhaps no improvement as all charts for the Vava'u Group in Tonga still seem to show the islands positioned about 1/2 miles too far west.
With due respect to the esteemed Captain Cook, there were other amazing navigators around, some much earlier. I was given a book about William Dampier who also had an interesting life, though with somewhat less probity than Cook. I believe that some of his sailing directions were still in Admiralty pilots until the 1920s.