User blog comment:Jimeee/Skyrim 1.9 beta update adds Legendary difficulty and raises level cap (Updated Apr 8th)/@comment-129.118.10.207-20130304232510/@comment-77.251.125.88-20130305160004

You'll probably get them all back to spend them in another skill, or you could keep them and re-spend them in the skill tree you made legendary. It's just a way to increase the overall amount of perks