Also the Legion of Superheroes books are not the only books from the previous books, the Bat-Family books also are intact, as is Batman, Inc when it returns. Also the present time Green Lantern books have characters and elements that have carried over.
Not exactly what I meant. The Batman and Green Lantern books have generally kept a version of their history, but they're still now in the new DC relaunch continuity. The new continuity has been merged into the Batman and Green Lantern books. Batman and Green Lantern will not notice that anything has changed.
From what I understand, the Legion of Super-Heroes book is still literally in the old continuity; they're not going to recognize the new past history. They will realize everything has changed.
Back onto the Time Trapper angle, one other thing has occurred to me. Who is one of the characters most changed in this relaunch? Superman. Time Trapper has been targeting Superman for awhile now because Superman is the inspiration for the Legion of Super-Heroes. If Superman was not as legendary, then the Legion may never be born.
The new relaunch Superman has had his support structure stripped from him. Both of his parents are dead. His marriage is gone. His ties to humanity are weakened. And with the time stream "closed" as Didio has put, Superman may have never had the Legion in his life.
Trapper has never had the ability to make drastic changes to past time (and in this case, the Trapper only took advantage of the can of worms Barry opened), but these nudges could be designed with the hope of Superman not finding his way to being such a grand hero and inspiration; thus the Legion would never form in the new continuity, and the Trapper would finally be free of its greatest adversary.