I mean come on that makes no sense at all!!
If this would be the case it would indicate there ARE skills which are PERMANENTLY active and you can NOT switch out, because obviously he asked if you could reset skills at at a point and Damien said "yes, but you loose the benefits you gained from places of power". It would make no sense if you could switch "builds" all the time that you loose the stuff from places of power every time you switch, that would discourage the experimentation with "builds", but they want you to experiment with them.
So my conclusions would be that there are active and passive skills. Active ones are the "builds" which can be switched around and have different effects while passive ones are the more "permanent" (probably stat-influencing) skills.
If that is NOT the case then I have no idea how this is supposed to work...