You remember this wrong. Jack didn't estimate their time of death, he said they died a long time ago because their clothes would have taken at least 50 years before decomposing.

Classic misguiding comment, to distract attention from the real clue that these two were linked to the "origins" of the island's mystery, the Adam and Eve comment. They've laid quite a few clues about the antiquity of their mystery, right from the pilot - but it's not before the ruins of temples and the Egyptian statue they were more open about it.

This isn't a retcon by the writers, the "adam and eve" foreshadowing and the fact these skeletons had the ancient playing stones in a primitive pouch with them is pretty solid evidence they've known all along these two were Jacob's female predecessor and his brother, especially that they had Locke elaborate on the antiquity of the backgammon game (Sennet, Royal Game of Ur etc.) in another early scene.