Okay. I tried all the tune options with egr off apart from stage 2. The ECM-44A0 comes back with them all as soon as the car is started.
Also there is now a code ECM-2BAA (Particulate trap. Value) and a particulate trap full message on the dash. Taking a long drive ~1h @ 80kmh did not make it go away so im assuming the regeneration does not work.
I also briefly tried EGR + DPF off tune which got rid of the DPF code but the EGR code was still present.