Will ECU/Flashing abuse your engine or affect the life longevity of the S?
I've had my S for over a year now, and I'm slowly modding it, performance wise.
Got a q300 and a K&n intake. I wanna make power gains, so I'm thinking about flashing it.

 

Yes it will affect longevity, if you do it correctly it may last longer.
A really bad tune on the other hand can blow your engine in very short time.

 

What this guys said. A good tune will make sure the air fuel ratio is and ignition are perfect for your car making it run stronger and safer, a bad one can mess them up and really do some damage.