You can install antitheft beta 2 as a root - just download the last public version, install rooted and then install the beta 2 with -r parameter, it will only update the app keeping the data.
The web registration is part of the installer and you can connect using existing account or create new one; so just use the existing one. You can see the your device twice on the portal - in this case you should delete the old one and repair the actual. In case you are flashing new ROM no information will be held about the account.