So, I chose tyrant and the three skills that follow (bad choice as it happens, the war leader ones are much better imo).
Then I did a ritual. This was a Vortex campaign, naturally.
When the ritual concluded... it was as if these skills stopped functioning entirely, until Malekith leveled up again. This lead to me losing about 4,000 income a turn for a while until I was able to level him up again. When I leveled him up and gave him another skill point - BAM! The income came back. I don't think any of his other skill points became disabled, because he still had his spells that I'd chosen for him. But the "tyrant" line was most certainly just turned off after that ritual was completed.