According to SE:

If I played FFXIV version 1.0, can I use a registration code attatched to a Windows version FINAL FANTASY XIV: A Realm Reborn Collector's Edition package?

If you played FFXIV version 1.0, you cannot use a registration code attached to a Windows version FINAL FANTASY XIV: A Realm Reborn Collector's Edition package. Instead, you simply need to purchase the Collector's Edition digital upgrade.

More details can be found in the following URL:
http://forum.square-enix.com/ffxiv/t...hase-Questions

For more on the digital upgrade, click the following URL:
http://support.na.square-enix.com/fa...68085&ret=main

If you have already purchased a Collector's Edition package, please note that we do not accept any returns. If this is the case, we advise you to create a new service account.
Source.

This isn't really acceptable though. I mean if we purchased the physical PS3 CE then we would be able to but not the PC? WTF SE, what are you thinking? What about the people who play only PC and decided this time around they wanted to get the PHYSICAL CE edition because they wanted not only the digital items but also the physical bonus items (such as the pre-order items, the soundtrack, artbook, etc...) as well as use their old v1.0 character? Apparently you didn't think about them and that's a real shame. You are creating a double standard by allowing those who purchased the PS3 physical CE to circumvent this, but not the PC users.