That'* a good question. I don't know about the Bonneville, but as a general rule of thumb, in most cars, the odometers are driven by the speedometer. Take the dashboard out of the car, and have a look on the back, near the speedometer. The odometers should be on their own little board, which you can pop out and inspect for damages; in your case, it may be a disconnected cable. It would either be a cable coming from the speed sensor in the transmission up to the speedometer/odometer.
EDIT: Forgot to show you this link. Sorry, no pictures. http://www.ibmwr.org/ktech/trip-odometer.shtml
As for your missing mileage, I'm not sure what to do -- either technologically or legally. I know rolling it back is a federal offense, but adjusting it forward. I'm no lawyer, so I won't offer legal advice. Worst case, you'll have to declare the vehicle as "mileage unknown" on the title. As far as technology goes, on some cars, I've heard of there being "backups" of the mileage stored in the computer, key, ABS system, transmission computer, radio, or someplace else. If the Bonneville has the mileage mirrored somewhere, see if someone can retrieve it.
Common sense alert: Remember that tampering with the non-trip odometer is a federal offense (well, at least rolling it back is). Don't poke around with it too much. If you manage to trip the anti-tamper mechanisms, white lines will show between the numbers (at least on GM'*), and the value of your car may plummet.