I also got two Early Access codes aswell, I ordered the digital CE from their EU store when it became available and got EA code later that day.
We get the EA code in a mail and don't have to go through the pre-order code registration to get it like the NA store.
Under my orders on the Store, Heavensward CE is still there and is registered as one of my games under my profile.

Confirmed by Bayohne;
http://forum.square-enix.com/ffxiv/t...=1#post2846130