If you can completely upload the data from your save file (on the cartridge) to your computer so you can use that save file on Pokecheck, without saving any data TO your cartridge, then it won't mess up your data. Personally, though, I'd avoid Pokegen, because I often get PID inaccuracies when I input accurate IV/Nature data, so I don't know if Pokecheck is more accurate in those terms.