Yup.
My petrol 2.5 L used quite some fuel during the break-in period; I used "Honest John's" (British!) method to carefully break-in the engine and I saw the mpg increasing, especially after 3.000 km.
From 10 Liters/100 km I went down to 8.5 Liters/100 km, so with your 2.0 you should even do...
If your car says "invalid card" it means that your cloning wasn't successful. Try to clone again.
As an alternative you can use : http://www.alexpage.de/usb-image-tool/
Or, of course, restore the backup that you made through the Toolbox.....