My understanding from the film was that there is no alternate timeline anymore. Rather, the passage of history is now that David is removed from Earth, taken to Phaelon for eight years, experiences the process of navigating his way back from the future, and then returns to within moments of his departure. He is the only David because there is only one timeline. The David who was sent to Phaelon at the beginning of the movie was returned, with a short side-trip into what is now no longer a future.
So, in short, David is taken from the Earth and has the star charts in his head. Eight years pass by on Earth as he is taken to Phaelon, studied, and returned over the course of a few hours for him. He returns to Earth and has his adventures in the Earth of eight years in the future. He convinces Max to let him use the hazardous time-travel method, and is popped back to shortly after he left (I don't believe that it is exactly established how much time has passed here, but the reactions of his parents don't seem to indicate that he's been gone the "hours" postulated for the original trip). The David who arrives is the same one who was abducted at the beginning and was briefly in a future.
Now that I look at the timing again, there's still some ambiguity going on in that they originally say that he spent hours going to Phaelon and being tested, but he seems to have arrived earlier than that. That suggests that it wasn't all just light-speed relativity at work (probably pretty much a given since they managed to go back after eight years. Relativity does not allow time travel into the past, just a slowing or even stopping of relative time) and that there may have technically been two Davids for the period of a few hours (one on Earth and one on Phalon, but the window would have been short, and there will be no David-A arriving in 8 years because that David is the one on Earth, David-B.