These are really basic questions that can be answered if you spend a little time reading. If you load a virgin EEPROM, you will lose the immo.
The EEPROM and flash are two different things. You must use the same file that belongs to the EEPROM, no cross-flashing.
Look:
>Either pull your EEPROM using Argdubs tool and fix the deathcode, flash back in bootmode the edited EEPROM. Then flash a proper checksum'd file to the ECU.
>Get a new ECU (same as yours) and code it in using the standard procedure on Ross-tech and code keys.
Choose one, and do it. It's pretty easy dude.