My experience (Minnesota), vehicles have 'VIN' and 'Serial Numbers'. All civilian vehicles after 1982? would have VINs that belong in a standard format. Custom vehicles, as well as some commercial (and military) will have a serial number.
The state MAY choose to re-vin the vehicle, in MN this involves placing a sticker on the A-pillar door sill, and then putting two custom metal rivets through the sticker to deter tampering. (The VIN sticker in MN is also just a serial number...)
For my HMMWV, MN (apparently, before I owned it) had inspected the vehicle.. verified the serial number of correct, and no other vehicles in the state had the same serial number -- so issued a title with a "short" VIN that happens to be my serial number.
Each state can do what they want with this... but likely your state has an 'override' policy. If you can show the original SD title with the short VIN to the right person, they can get that serial number approved instead of a VIN.
EDIT: Forgot to add, some states may require a vehicle inspection for a non-standard VIN. In Minnesota this inspection is done by the state patrol. I have a 1967 Jeepster Commando I went through this process with. The annoying bit was no on-road registration meant I had to have it towed to the inspection area -- leave it with them for a day, and then get the approval letter. (And in my case, they also added the VIN sticker since they didn't trust the serial number plate held on with [factory original] Philips screws.)