Remember Phantasy Star Zero? ;<
What about it? While the game took place on the planet that Pioneer 1 and 2 were from, it took place long after the events of PSO, to the point where none of the events of PSO have any affects or bearing on the plot of Zero, other than the fact that it takes place on Coral, the planet that Pioneer 1 and 2 hailed from.
Zero is, for all intents and purposes, it's own self contained story that was originally supposed to be something of a reboot of the series. It's more or less the same with what they're doing with NGS. While the game takes place in the same fictional universe as PSO2, the setting of the game is so far removed from the events of PSO2, that it may as well be in it's own different universe ala the other games in the series.
I mean some of the characters could be in cryo-sleep until NGS, which I would assume would be the case for your character.
Unless they do something like XIV did with carry over characters from 1.0 into 2.0, that's probably not going to happen. Sega already explained that the protagonist of NGS (that is, your character) is an amnesiatic Meteorn that, like all Meteorn before them, fell from the sky and awoke to fight the Dolls that are plaguing the planet.
Chances are the carry over from PSO2 into NGS is just going to be strictly for gameplay reasons so players don't lose the years of investment they put into the game going into NGS, which frankly is a pretty intelligent move for Sega to make as opposed to simply making New Genesis it's own stand alone game.