I got a reply from the EU support for the ticket I made about this issue. Basically its telling me I'm stuck with codes which are useless and I paid for, and if I want my items I'm going to have to pay extra.

We are sorry to hear of your issues registering your Collector?s Edition code for FINAL FANTASY XIV: A Realm Reborn.

Unfortunately, it is not possible to register a Collector?s Edition PC code if you already have any PC version of the original game already registered.

If you registered the Collector?s Edition code, it would create a new service account, but it would not be possible to transfer any of your characters to this.

The only option to upgrade your existing account would be to use the Digital Upgrade service available on the Mog Station.

We apologise for the inconvenience and hope that you will enjoy playing Final Fantasy XIV: A Realm Reborn!
I'm a patient person, and I can deal with all the server down time and all. But when There is clearly a problem at the SE end of things here and we, the people who have given them a second chance and are willing to spend more money on a CE, get screwed by their system really pisses me off. Very poor service SE, very poor.