There is a bug with retraining tome not always resetting your skill points. I have encountered it 5 times when i tried to reskill Archmage from water elemental/aura - after using the tome, the water elemental skill stays.
It’s because your water elemental ability is still on cooldown. You need to wait for CD to clear before using it
That’s a good point. It still doesn’t work as intended I believe.