The quest achievements are not removed, it just resets your quest achievement tracker to 0 again. Or you will only track the quests that both factions can get, like ratchet quests. So in other words I achieved 250 quests achievement with my home faction, but because horde doesn't have 500 total quests, when I faction changed, my tracker reset in my achievements interface. I can't remember exactly how many I was showing, but I think it was under 50. So I can still get the 500 quests achievement, because ally side has over 500 total, but i need to do all of the ally quests to get it. In other words the two don't add together. Which kinda bummed me out. Hope that helps.
