I bought a 2005 103 fat boy which has a heavy breather. It also had V&H Big Radius fitted but I had the dealer put on the original SE2 pipes which, now they are fitted I find has no baffles so back pressure will be wrong. The dealer claims the bike has no tuner fitted, yet it seems to run very nicely with just a small amount of decel popping. What gives? Could it have been recalibrated somehow without a Pro Tuner or similar? Or am I going to stuff the motor? It used to backfire with the V&H but not now.

Taffy, from what I know the baffles would  reduce the noise coming out and increase horsepower if you know where to place it in the muffler,  since the original SE exhaust was set up for your 103 engine it doesn't need to be recalibrated as the exhaust with it's muffler and length provide the correct backpressure for gases to exit.  The V&H you had on previously a tuner of some sort would be needed to stop the popping as the exhaust gases would exit differently due to it's different length and size compared to the SE pipes.