I'm assuming this is a bug. As you know there are "trainers" scattered around the game that can boost some of your skills if you pay them 3000 coins. In my case I had paid Granis Yirgar (found inside the palace in Serpent's Crown) to boost my Survival and Athletics skills. After I retrained my main character (reset to level 1) Granis' training bonuses were lost. When I returned to Granis to see if I'd be able gain back his bonus he simply said he had taught me everything he knew.
Is this a bug or is it intended?
Edit: Apparently I put this in the wrong forum section, because this happened for me in the current build, not in the beta patch.