I know that both were destroyed in the final scene of the chase ; the first Charger overshot the gas station , so the second "backup car" had to be employed for the re-shoot , thusly destroying it in the process
That is one of the rumors but the other is that the real R/T car was also used as the Camera Car. The other half of the rumor:
Now that being said there was NO documentation from Warner Bros about the VIN numbers on the cars used in the movie. So technically it can never be 100% proven.