Larry, not sure of your level of technical aptitude so take no offense if you already understand this: There's a computer on your bike called an ECU (Electronic Control Unit). On that ECU is a piece of software that controls when your fuel injectors spray fuel into the engine, how much they spray into the engine, etc. based on a load of different conditions like engine RPM, load, throttle position, and more. The flash tool is simply the conduit that allows you to copy over that software with updated software that Todd supplies. The decisions Todd makes about what bits of that software to modify to give you better performance are done with the assumption that you have already removed the evap canister and tip valve. If you load Todd's program to your bike and fail to remove the evap canister and tip valve, the new software that Todd has supplied will not work to maximum effectiveness on your bike.
While the evap canister and tip valve serve their purpose as part of the emissions system, it comes at the expense of ride-ability. That evap canister system effectively creates a vacuum leak in your intake system, which is not conducive to performance or smooth riding enjoyment. The removal of that system works hand in hand with Todd's ECU reprogramming. So if you've gone to the trouble and expense of purchasing the flash tool and loading up Todd's software modifications you really should take that last step and eliminate the evap canister and tip valve. It's about a 15 minute job.