It is my personal opinion that skill points should be returned/refunded, if you do a quest that gives skills that you had previously purchased from a trainer. Otherwise i would suppose we are to walk around endlessly looking for quest givers, and to twart the immediate response that then quests would be ignored, i feel that would make players infact focus more on quests knowing that even if they had already bought the skill, that they in minimal would recieve a skill point back from the quests or however many skill points were thereby earned by purchasing skills that the trainer would have given.
Next i suppose people would state that what about the old players that are in this boat, well Arena.net most likely tracks the quests that you have completed and therefore would simply be able to give you the amount of skill points you previously earned from said quests in this previous situation.
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R

. Don't take it offensively, your post is rather constructive, I'm just like that sometimes.