Is it possible to flash a 2.7 S4 file to a 2.7 A6 box? If it has the same chip I'm sure you can do it but are the other chips on the ECU that are car specific? I would be using an ebay cable and Nefmoto flasher through OBDII. Looking for an inexpensive way to have a back up ECU in case I brick mine.
Thanks!

No I dont believe NA S4s have an immobilizer but if an A6 has one and I want to use an A6 ECU what would I need to do to the A6 ECU.

I am not sure what info is help in the eeprom, would there be an immobilizer ID verification process that comes from the A6 ECU? I take it the eeprom does more base level functions while the flash chip hold the engine maps. Is that correct?

Thanks Julex, But my situation is actually opposite. I have an S4 and want to use an A6 ECU as they are more available and cheaper from junk yards.  I have seen a thread that talks about flashing and A6 ECU with S4 engine maps but they were using a Galetto and didnt mention anything about reflashing eeprom info, how to do that, or if it is even necessary. I imagine if the ECU is requiring an immo and the S4 doesnt have one then it wont start so I would need to bypass the A6 immo or completely swap eeprom data which sounds better anyway. I am trying to figure out if thats all that needs to be done or if there are other chips that would interfere with that.

Just seeing if anyone has done this or know if its possible before I thrown more money down the Audi toilet

could there be other reasons the car won't start? do the files contain the same maf tables?
When we flashed an s4 file to an allroad ecu (4Z7907551M) the car started but died due to the immo. after the immo was disabled the allroad ran like a champ.
did you validate the memory layout?
which memory layout did you use?

AFAIK 2003 A6 has BEL engine and 7.1.1 motronic, just like Allroad? No wonder it didn't work.

I will soon clarify the situation with ECUs. Right now I am running Allroad 4Z7907551 ECU (no letter after part ID) flashed with what seems to be M-Box S4 tune file.

When accessing ECU the "Extra" info field is blank and block 81-82 immbilizer ID fields are blank as well. What his means is that the flashed wiped out immo info from ECU...

Prior to blasting S4 tune on it both fields 100% contained relevant info with my VIN and immo ID.

I experimented with the key and put a large steel plate between the key fob and ignition and turned/started the car. The plate 100% blocked EM field so key couldn't respond. No reaction from cluster/ECU and car started just fine...

I think this proves that the immo stuff actually sits in programming of ECU not in separate chip as I thought previously.

I will experiment more to prove or discprove that, I will be flashing spare Audi A6 with Immo3 with S4 another S4 tune soon and plugging into my allroad. If the car starts then it definitely proves that once you insert your own BIN, the immo is gone.

Edit:
Took apart my key and used just the blade to start the car. With original cluster, original hardware ECU box and S4 tune, the blade would start the car and I could drive albeit with flashing "key" icon which with fully functioning Allroad BIN would not allow me to operate the car. I believe the flashing icon was because the cluster is the mediator of immo code and it couldn't get it from the key.

Once a cluster obtains the code it passes it to ECU, which in turn either accepts it and allows the car to operate or sends signal to cluster to pop the Icon. S4 doesn't have immo routines so it just ignores that particular message and doesn't ask cluster to pop the icon.

It looks like you can use any ME7.1, being it from S4, A6 or Allroad and you'll be fine on S4. Moreover, any A6/Allroad user can use any box as well and flash S4 tune but will loose immo protection.

Depending on UPS, I might have an A6 ECU with completely different immo code on it in today and will see if flashing this guy with S4 tune works ok. It should be a pretty good test since my allroad has immo3 in the cluster. If it works the way I think it will, e.g. immo in ECU will get neutered by S4 tune, I should be able to just start the car and go my merry way...

Will keep posted.

Tip ECU with 6 speed software? Yes.