Several years ago when I had my Audi I hit some very deep (8 inches or more) standing water at a very good rate of speed (uh, about 50-60 MPH) and ended up with a noise kind of like what you describe. WHat happened was the water pressure bent one of my heat shields all to hell and it was rubbing on my rearward driveshaft. It was worse when decelerating because of changes in the angles, but the idea was the same. I guess it kind of sounded like cards in bicycle spokes, but more metallic. Hard to explain.
Anyway, perhaps the dealer bent a heat shield or such while working on the gearbox and it is rubbing on the driveshaft?