The phone's registration automatically expires after 1 year, that's probably the problem your facing. Though I'm not sure why you can't re-register it directly using the registration tool.
To solve this issue:
- Go on the Windows Phone Dev Center website and log-in
- Go the devices management page (click on your live id in the top right corner, then on "Phones")
- Search your phone in the list and click on "Remove"
- Launch the Developer Phone Registration tool to re-register your phone