I had the same issue. The first time, i had to call the 800 number and have them deregister the device from my account. They give you the run around about what caused them problem. Just plead ignorance, or tell them that the device reset. Or you could tell them that you were rooted and want to go back to stock but cannot re-register...not sure they would take too kindly to that?
The next time I wanted to deregister was after I went over to the CM7 ROM. After flashing CM7, I wanted to deregister the device, so restored a nandroid of rooted stock and proceeded to deregister. Then I restored CM7. If you have a nandroid with your registration in tact, that might work for you (but may require re-rooting).
I think that the rooting instructions for non-stock ROMs should include instructions to deregister the device before flashing to avoid these complications. It seems like the restore to stock instructions should also include a step to deregister the device before preceding with the un-rooting process. Apparently, you used to be able to deregister through the BN website, but that is no longer an option. So this seems to be more of an issue. Good luck.