I think the issue here is that you have an AT&T iPhone that was unlocked via 3rd Party, having them replace it will get you another AT&T iPhone, and you will likely lose your unlock.
When they replaced mine, they took the sim card out of the old one and just put it in the new one. As far as registering the IMEI, I think you are talking about registering the SIM ID (I cant remember what its called) which is used if you are switching sim cards. I don't think anything will happen if you were to swap sim cards from phones, other than the fact that the replacement you are getting may very well still be locked, even though you maybe getting an AWS model. If anything, you may want to tell them that it was unlocked by AT&T
For anyone still on the fence or haven't done this yet, and still want the AWS model and still have a pristine non-AWS (unlocked) iPhone, but aren't sure what to say, show the genius the support article,
http://support.apple.com/kb/HT5720. Let them know that you are experiencing poor data services in x location, and that the article explains why. You'll do a service by educating the geniuses since it seems none of them really know about it, and they cant really say its "fake" or anything like that since its on their official support manual.