So, i was playing PvP yesterday and crashed - happens (should not, but i guess we are used to it by now).
After i got back in, messages about skill lines gained flooded my screen and i after checking i noticed that my progress in the alliance skill line was gone. RESET TO 0!
The skillpoints still have been spent, all skills are on max level, all passives filled ("2/2") - but over everything was the locked symbol...
So cudos for this original bug, ZOS!
Fix your game.
Wrote a ticket, i hope you can unlock the skill lines again!