In addition to the main larger flash memory that holds all the ECU tuning tables, ECU also has a separate smaller EEPROM memory which stores some of the other configuration data such as the VIN and immobilizer.
The ME7_EEPROM tool can be used to read, make changes and (boot mode) write the EEPROM memory.
http://nefariousmotorsports.com/forum/index.php?board=42.0 If the EEPROM command line program is difficult for you to use, there is also a GUI for it bundled in the ME7 visual logger that is a bit more user friendly.