Yeah, your situation is a bit more odd, since you used the same HD...

Way back when I was playing Two Worlds and managed to destroy that game as far as the achievements went, but I played the whole game offline. Later, I went to transfer my profile to another xbox, which had Live, and my profile updated. Since I had played all of Two Worlds offline, it actually took away all of my achievements and there was no way for me to get them back because my save file acknowledged me completing the necessary objectives in order to get the achievements. So, short of starting all over again, there was nothing I could do. 900 cheevo points gone and the game sucked too much for me to want to play it again.

Same thing happened to a friend of mine playing Dead Rising. Basically, just play everything while you're connected to Live and you won't run into cheevo problems.