The baffles in the exhaust system of Harley-Davidson's FLSTC perform a dual function. The design of the baffle reduces and disperses the pressure pulses from the engine, thereby reducing the volume of the exhaust report. They also provide a certain amount of backpressure in the exhaust system, which is necessary for maintaining the air-fuel mixture and preventing exhaust-gas reversion.
When you remove the baffles, the lack of backpressure allows exhaust-gas reversion to occur, which means that exhaust gases will curl around in the exhaust stream and re-enter the combustion chamber where it mixes with the fresh air-fuel charge. This can sap power by as much as 15 percent. The loss of backpressure also causes the engine to run lean, which can lead to damaged plugs, scored cylinders, and when coupled with carbon buildup on the piston crown, can melt and blow a hole through the piston and ruin the engine when the aluminum slag makes it into the roller bearings in the lower end.
When removing the baffles -- or preferably replacing the exhaust with a low-resistance system -- you must increase the intake air capacity with a low-resistance air filter. In addition, increase the size of the main jet and intermediate jet to maintain a proper air-fuel ratio. The exact size of the jets will depend upon the other modification you perform. If you have a late-model FLSTC with fuel injection, you'll need to have the injector-system output increased in lieu of changing the carburetor jets.