According to one of the brotherhood scrolls, the time machine's power is temporary(you can see the hands on the clock winding down indicating that it wont last long) and only affects the surrounding area (mainly the portal tower) so they're still in they're present time. So by the time Gabriel defeats the forgotton One the tower will return in it's present state of being destroyed.
Edit: I just realized something, now that Gabriel has undead powers, wouldn't that mean that using the combat cross would be dangerous to him now?