Khan, The 37s, Gillian Taylor, Isaac Newton, Mark Twain, Maury Ginsberg and I'm sure many others who aren't coming to mind now are humans who left Earth by various means before Warp Drive.there's no way Flint could have left Earth before the invention of warp drive in 2063.
Plenty of other methods where he could of too. Vulcan survey ships as in carbon creek, the Aegis, however Guinan got to Earth, any of these people could pick up on an immortal even if he was concealing it from the rest of technologically limited humanity.