The only thing it will affect software wise is the speed readout as that's determined by multiplying the RPM of the wheel or motor (not sure if it uses the ABS sensor like an ICE bike or not) by the circumference of the wheel. An FX tyre has a circumference of 80.3 inches and the FXS tyre is 77.7 inches, so the speedo will read slow by something like 3%. That means at 60mph you'll be reading 58mph so not really a massive difference, obviously it'll be even smaller at lower speeds and a bit larger at higher ones (2.6mph lower at the 85mph top speed). You will in turn gain a tiny bit of torque at the wheel.
The bigger difference is going to be the geometry change, the front wheel will 4.3 inches smaller in diameter resulting in the axle dropping by over 2 inches and steepening the head angle and shortening the trail. I'm not that knowledgeable when it comes to geometry but I believe this will make the bike less stable but turn easier, so could be good or bad. The FXS actually has a shorter travel fork than the FX although I'm not sure if it's overall length is shorter, if it is then handling will be somewhere in between an FX and FXS.