Hmm have you had a rolling road check (not sure if you can do this on a diesel - sorry i'm a petrolhead not diesel).
As it maybe some other component that may be faulty causing the flat spot not the ECU.
As the ECU is just relying on bring back sensor values to perform calculations to give you that extra umph.
Was at a dealer yesterday - I asked about how they decide to reload or update s/w. He told me they reload if a fault is found or reported by a customer.