Response to my request to fix up this mess from the Support Centre.

"Thank you for contacting the Square Enix Support Centre.


We are sorry to hear of your account issues.

Unfortunately, as you already have FINAL FANTASY XIV: A Realm Reborn registered to service account 1, it would not be possible to move the game from service account 2 as it is not possible to have two copies of the game registered to one service account.

The option you would have would be to use the digital upgrade service on service account 1 or create a new character with the Collector's Edition content on service account 2.

We apologise for any inconvenience caused."

So according to SE's response it seems lots of people just got screwed for buying the boxed copy of the CE if they already had a FFXIV 1.0 standard version of the game.