for this first quote, i changed ivs, evs, moves, nature and hability of one pkmn and made 5 shiny, something was wrong and every time i get to pc, my 3ds crashed and rebooted....
the answer to my own problem:
Run pcdata.exe at prompt:
Go to your PCdumper folder and type this this. "C: \whatever....\PCdumper\pcdata.exe in" and (dont close the prompt window)
Open PKHeX
Drag and drop savefile in PKHeX.
Edit your boxes
To export, click on the right side the "SAV" folder, click "export SAV", and choose your PCdumper folder.
Return to the prompt window and type "pcdata.exe out" so your prompt should look like this "C: \whatever.....\PCdumper\pcdata.exe out"
Copy pcdata.bin back to the 3DS SD card.
i dont know why the pcdata.exe is not working right, maybe if you post the source code, we can see exactly what is doing...