The ECM is only one part of the issue. The TCM is recording data also. Maybe a torque curve or excelleration value or ......hmmmmmm! Unfortunatly the LMM is about to be scrutinized because of the DPF. The LBZ has the same capability but probably will not be used in the same way.
BCM and SIR can also play a part. The thoughts of just swapping the ECM with a stock one won't really mask the modifications if the technician knows where to look. If not then you should be good to go.
If I owned a LMM...I would not throw the DPF away just yet. You may need it again in the near future.