Can this ECU flash be done without voiding warranty, if it makes that much of a difference i would like to do that even before thinking about exhaust changes?
That depends on Suzuki HQ being asked by you to replace a failed engine or ECU.
You should expect a failed engine to be replaced with a crate one or even a new complete bike; and with your's striped down here or Japan to find exactly why, if it was not obvious.
The Factory would definitely be wanting to download all the files from an ECU for it's history.
Normal basic Dealer servicing won't show that an ECU has a remapped fueling but things like Deceleration Fuel Cut, 02 sensor disabled are visible with the right software that servicing needs to be using today.
Warranty is offered by Suzuki and everyone else too is based on what they made, being kept exactly the same.
You would have to prove beyond doubt that your modification did not cause the failure, and did not contribute materially to it. That's the way Companies see it.
With the ridiculously short 12 month USA Warranty offered, your limited exposure time to consider this a "possibility " in my view is well worth taking IF you are using an experienced ECU GSX-S Flasher like Dano's in the USA.
The reality is the motor will be fine. The worst case is a bricked ECU in the hands of an amateur.