This question remains unanswered to me. Since 4.0.3a hit, there are lotsa quests to be done and I want to do them for achievements, but I'm afraid I will lose guild exp/rep(?).
well i dont see how you would lose guild exp/rep seeing as cata hasent even come out yet, and even then you woudent lose any. you get the exp/rep by doing raids/instances with people from your guild. from what i know there is no way to lose guild rep besides the obvious (leaving the guild).