To expand on this slightly.. (and hopefully no one flips out like the last thread).
Flashing is possible through the port on a 2010+ ecu in every region. The issue is that the ecu (in some regions) is capable of detecting modified code and will lock the ecu down if it is installed, basically car will not start after being flashed, but it can be flashed.
The procedure most tuners are doing is not actually a bench flash but a separate process entirely that is simply reading out that code which locks the ecu, modifying it and then putting it back in. That must be done on the bench as there is no access to that area of the ecu through the port. Once the ecu is "unlocked" it can then be flashed on the bench or reinstalled in the car and flashed through the port either method works. Bench flashing actually requires corrupting the file to force the ecu to accept a new flash so even though we have the ability I generally instruct my dealers to do it in the car. Never once had a problem by why risk it right?
Depending on how the tuner went about unlocking the ecu some are compatible with another tuners files some are not. The best way to describe it is there is a short way and a long way to unlock the ecu, neither is right or wrong just two ways to get the same result. If a tuners files are built to work with the short and the previous tuner used the long method the second tuners files most likely will not work and the ecu would be locked (car won't start) until it is flashed with a true stock file. Again nothing wrong with the different methods.
As i just mentioned flashing an ecu back to stock would recover it. That is because using a stock file resets any of the unlocking that was done and you are basically back to square one. This is why a home flashing unit won't work for the later applications. Even if you sent the tuner your ecu and they unlocked it, if you were to ever reflash it to stock the ecu would lock and would need to be sent out again.
When the ecu is unlocked and not even flashed yet the checksums change, this is visible to your dealer on later ecus but I have never heard of one dealer keeping tabs on what the values are and using this to deny a claim. I have heard in some cases VW flagging cars when this is noticed in diagnostic logs, however not one single instance has been reported to me of a Revo car being flagged nor have I ever heard a flagged car having anything denied. When speaking to a friend of mine who does software through his VW dealer he just said that VW wants to you do your due diligence before they accept a claim but they are not outright denying or even voiding warranties and he had not had one single problem yet.
The only way to make the tune 100% invisible at this point is to flash a modified ecu back to 100% stock. To reinstall the performance software you would need to have the ecu removed, opened, and "unlocked" again. Regardless of your tuner.
For tuners who have switchable software such as ourselves in stock mode the car will appear stock, drive stock, and other then the checksums to a dealer be stock. They can flash over it (which will erase the tune and unlocking), they have full diagnostic access to the ecu, and well bottom line nothing really changes.
Now my personal opinion based on 10+ years in the business both as a dealer tech and working in the performance industry including owning a shop. VW is not voiding warranties. What you may hear on the forums is simply people who were denied service at dealer A because the dealer did not want to risk having a claim denied and paying for it out of pocket. Your warranty is a contract between you and VW, not the dealer and they have no right to void your warranty on their own if they don't like your wheels or your intake. If you are denied service at dealer A go to dealer B, chances are you will have no problem. While working at both VW and audi dealers I know of only two instances where a warranty was void and it was just on very specific parts. One was a personal friend of mine who raced his GTI VR6 running nitrous. He was blowing through transmissions. The VW rep knew he raced, knew he used nitrous and let a few claims through. At some point he was told that they need to pull the plug. This friend had an actual contract from VW stating what parts were still warrantiable and which were not. The other was an Rs4 (possibly just S4) that kept breaking clutches and axles. This kid tried to deny he was racing it but kept dropping the car off with remnants of shoe polish on his windows from numbers and often times time slips still in his door pockets... not very smart. I think one clutch and an axle or two where covered no problems. Eventually again Audi said wait no way. His warranty was voided only on the parts he specifically kept damaging and had documentation regarding this.
Also this is 2011, VW doesn't give a crap if you modify your car. The ignorant dealer tech who wants to get paid cash rates instead of warranty rates is just looking to blame your mods so he can make a few more bucks. I've worked with these people at every dealer, when they tried this I always jumped in and stood up for the customer with the manager and usually won. Request another tech or find another dealer if this happens. Dealer techs now often come into that job because they love cars and love modifying them, it is no longer should be be a fry cook or maybe work on cars. Chances are half the employee lot at any dealer is filled with cars ranging from a basic flash to upgraded turbos.
There are times when people are just stupid.. screwing wood screws into your floor to install an amp is NOT something covered under warranty when you poke a hole in the fuel tank. You snap studs on your turbo putting in a downpipe.. this is not something covered under warranty. Tunes have never proven to actually cause a problem of any sort especially in these applications where boost pressures are barely changed and even fuel pressure remains within stock limits.