I had the same thing on my rogue. I have the '2000 quests completed' achievement, I was actually at about 2900/3000 for 'Seeker', now after the transfer I'm down to 950/3000 completed on the 'Seeker' achievement. Sigh. I'll probably never get that one done.
Also, my Eastern Kingdoms and Kalimdor Loremaster achievements are now at like 50-100 quests complete out of 700 required. YIKES! Same with all the outland zones, many of them I was within 5-10 quests of the zone quest achievement, now I'd have to do the entire damn zone over again to get the achievement...
And my 100 Dalaran Cooking Awards achievement got reset to 0/100, even though I was at 97/100 before.
And my armory of achievements still lists alliance achievements for me, although in-game it shows the proper horde achievements. It also fails to list some achievements as complete that do show up as complete in-game, example "Our Daily Bread" (complete all five Dalaran daily cooking quests). In-game I have alot more of my Cooking achievements done than what the armory shows...
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