Since the skills that a character has can change during the game, they are stored in the savegame.
Even if you change the initial skill set (which is what you can really set in the editor), the skills the character is now (in your savegame) supposed to have may have changed.
You could add the missing skills from Story on game load.
https://docs.larian.game/Modding:_Versioning#Story.2FOsiris