Can you expand on that
@T-800
There is no "flag" inside your ecu as such.....
The "TD1 Flag" is actually a flag on the internal VAG car database not physically (or electronically) in the vehicle itself and can be added to a cars chassis number manually by a dealer for a number of reasons:
Basically if they feel they have sufficient evidence that the vehicle has been tuned/modified they can add the TD1 eg. physical evidence the ECU has been opened, excessive flash counter value, File verification via the GEKO server, Boost and injection quantity logging, Tuning box related DTC's, aftermarket exhaust, suspension etc.
Once the TD1 is added, any dealer query on that particular chassis number will show that there is a TD1 flag stored against that vehicle, and thus any drive train related warranty claim
could be called into question depending on the dealer. It isn't an automatic VOID of your warranty as some would suggest, its simply a flag to alert the dealer working on your car that it has been modified and my require different diagnostic procedures to a standard car.
Flashing your car will increment the flash counter in your ECU so a savvy dealer could possibly question you regarding this - there is no way around it I'm afraid. But with that said, it certainly doesn't mean an automatic TD1 flag will be raised against your car.
If the dealer goes looking specifically they
may see that the flash counter has incremented which in turn
could raise their suspicions regarding whether the car has been tuned (unlikely to get a TD1 flag for this alone).
Further to that they
could request a software verification via the GEKO server in Germany which will check to see if the software inside your ECU has an original Volkswagen AG certified checksum/RSA signature (which of course it will not if you are running a modified file but will if you have flashed back to stock)