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-184.88.24.236-20130305004233

Sounds like you'll have to fight to get them back; This will reset the skill to 15, return its perks and allow the skill to affect leveling again.

IDK if they will remain so you can put it to something else. Would be nice to have more perks available.