Something very similar to changing the ECU on an Airbus was implicated in the Spanish Airbus military version crash. exact details escape my mind now but the crate flew with 'non flight' configurations.
In this case the engine control appears to have had a sort of Road Plan and Test Plan and was able to opt in to either mode as circumstances 'required'. Apart from those down stream of the tail pipe (more or less everyone) the operational safety implications look likely to be zero.
Biting the hand that feeds IT
