The ATA assessment will be per vehicle regardless if the vehicle is replaced or not. In the end, you would collect .50 for the old vehicle and .50 for the new vehicle during that reporting period.
Example: VIN 999 is the only vehicle on a policy written in Sep. That vehicle was replaced with VIN 8888 in Dec. The ATA would collect .50 on both vehicles for a total of 1.00, or would that just be .50 since it is only one vehicle.