When you added the Security Token to your account, you set up an emergency removal password. I'm not sure if you can change this, if you've forgotten it.

When (if!) the battery ever runs out (or you lose it like I did) you go to https://secure.square-enix.com/accou...vc/coercioncan (linked off the login screen) to remove it with that password. You can then register a new one or register the smartphone app.

You can't ever re-register your old token though - I'd lost the one I bought when they were first released for FFXI, searched everywhere for a week, before giving in and using my 1.0 CE token. I found my XI one a few weeks later in the fireplace :x Bloody kids. It's now sitting in my 1.0 CE box - I've just checked and it still works!