Whichever skill was last selected to specialise in.
E.g. If I choose the Focus skill as a specialisation (i.e. select the skill at the top so that I can put points into it’s tree), add one or multiple points, then the next time I open the game, the points in that skills skill tree will have been reset/refunded. I’ll still have the points to spend (skill is the same level). It seems to only happen the first time a skill is selected per specialisation slot. So if I then switch Focus to another skill and add points, they won’t be reset when I restart the game.
This actually just happened again on my Acolyte:
In the above instance I had gotten to level 8 and exited the game. I just started up the game today and the points are reset.
For further testing, I just levelled up to 9 to get my next skill specialisation slot unlocked, added 1 point, exited the game again and then opened it again and the the point was still there! So I’m either wrong about it resetting after restarting the game or it’s just inconsistent or maybe it only happens when I restart my PC as well.
When I can, I’ll wait till I get my next skill specialisation slot unlocked, add a point then restart my PC to see if it happens again.