Does Save Dongle, Powersave and Pkhex affects the data of the cartridge?

I am planning to reset all my games (XY and ORAS) to the original stage (Initial stage with no data) before Pokemon Sun & Moon comes out. May I know, does my usage of Save Dongle, Powersave and Pkhex in my games affect the data of the cartridge? (which means even if I reset the games, somewhere in the data is still being compromised and it is no like a new cartridge that has never being hacked?)

Thank you for your help.

You could probably use a save dongle or powersaves to do that, but IIRC, there's a button combo that can erase the save. It should be somewhere in the manual.