User blog comment:Jimeee/Skyrim 1.9 beta update adds Legendary difficulty and raises level cap (Updated Apr 8th)/@comment-79.25.127.87-20130326170751/@comment-4804021-20130326192142

The perks you used in the tree should be given back to you when  you decide to make a tree legendary. I haven't played, yet. But that is what I have gathered from those who have played. If not, just spend a dragon soul with the DLC Dragonborn and reallocate the perks before you make a tree legendary.