Any CE you purchase will automatically upgrade the FFXIV service account itself to CE status (2.0 CE status; Heavensward, an upcoming expansion, will have its own standard and CE versions much like the base game does now).

Any versions you buy thereafter simply grant access to play those version-specific platforms; you'll still retain the CE status of the account.

For example, I already had 1.0 CE status since I purchased XIV 1.0's CE in 2011. I have, since then, purchased a PS4 standard version. My account reads that it is still CE status after having used said code in the PS4 version.