Cummins did the same thing years ago with the 24 valve engines in the dodge pickups. My 99 had a recall to be reflashed after they were caught doing the same thing as volkswagen. I took it in and had it reflashed and didn't notice any noticeable power reduction or mileage penalty.
However, that was 16 years ago and the emissions standards were much less tight than now. There's no telling what a reflash will do to a volkswagen TDI. At a minimum I'd wait until owners reports start rolling in about what it actually does to mileage and power. The big question is whether the government, either state or federal, puts in place some kind of regulation that says tags can't be renewed or the vehicles registered without the reflash. That would make them unsaleable unless you have it flashed. In states with diesel emissions testing it's pretty much guaranteed that they'll not pass you on the test unless you have it reflashed. Fortunately my home state of Mississippi doesn't have any emissions testing so if I owned one I could probably go without getting it recalled. I'll bet that someone living in a place like California or New York is going to be forced to have it done or they'll have to park the vehicle.
