My interpretation of the "reboot" is that the DnA Legion is now adrift in the timestream, looking for their way home. Although I doubt that we'll see them again, the possibility exists.
The new Legion, I think, is a different plane of reality (or perhaps Hypertime) than the DnA Legion. Now, with time travel being as flukey as it is, I think that you can agrue that this is the "new" future of the DCU, or perhaps that this is the way the future was always meant to be, and that the DnA version was an alternate.
As reboots go, I think it was fair in that both versions are real and neither erases the other, unlike the Zero Hour reboot, or even Crisis on Infinite Earths.