Having the same exact thing happening in my Daniel campaign.
Taking the Khorne Legendary Lords as refugees makes the blue skills disappear
(not even visible on the talent tree).
Resetting the Skill Points does nothing to fix it, it remains the same as well.
When I start a campaign as a Khorne Lord they work just fine with all skills visible.
The only other mod affecting Lord Skills I have is Singe's Lord Skills Compilation.
Don't know why this is happening.
Otherwise loving the mod!