You'll get a DTC for the VIN on the ECM not matching the VIN on the other modules on the vehicle. You also have to divorce your smart key module from your old ECM to your new (used) ECM, which I'm not even sure is possible with a used ECM with a different VIN # on it as I've never tried it personally. I've always just been told it wouldn't work by people that do these things more often than I do, so I believe them.
To top it all off, every time you try to marry your smart key module to your new/used ECM, there's a chance your smart key module will commit sudoku and off itself (yes I misspelt that on purpose) even when pairing to a brand new ECM, which means you now have to spend several hundred dollars replacing that module as well.
So I've officially programmed the second (tuned) ECM to the car, and still managed to have the original ECM work just fine with just plugging it back in
I had to De-register the new ECM again before programming the Smart Keys to it, didn't have to do anything else to the original ECM. I can freely swap back and forth between the original and the tuned ECM now. Guess those guys I spoke to were not completely correct (luckily for us)!