I am going through the same thing with my Audi at the moment which definitely adds a write cycle flag when the ecu is written to, some software is able to remove that flag but most tuners aren't aware/aren't capable of doing so. I bought a replacement ecu from ebay which would get around the issue, 10 miutes to swap and return the car to stock but at the moment I'm struggling to get someone who can copy the immobilser fromm the old to the new ECU.
The only way around it is a chip tuning box which used to justifidly have a bad reputation, hoever the new generation ones such as those available from DTUK are far more advanced. My brother just added one to his new company car at around 1000 miles old, we did a before and after run on a rolling road and it genuinly added the 40bhp promised to his original 140 and a road test showed a much improved drive and seems like better economy but its only done 2000 miles now so very early days.
How well they work on the Euro6 engines though? DTUK do a moeny back guarantee so not much to lose and a £45 rolling road run would confirm the claims or not.