Quoting from FFXIV Steam news:
So, Steam users will need to purchase everything again or? It seems that Steam won't accept the activation codes from the physical CE?Greetings, Adventurers!
The time is finally upon us – the realm of Eorzea will see its first expansion, and it’s going Heavensward! As you probably know, pre-orders have started today at some retailers.
Fear not, the Steam version will also be available in the future. In the meantime, please keep in mind that you can only upgrade your Steam-version of A Realm Reborn via a Steam version of Heavensward – others just won’t do!
We will definitely keep you informed on when the Steam pre-orders go live, so keep your eyes on the Community Hub!
Your FFXIV Community Team