Before writing the game to sdcard with disk writer edit the template to use the same header from where the game that save comes from. And make sure save is from the same 3ds.
I made such a program, it's in a thread here.... Wait
Here:
http://gbatemp.net/attachments/skysavetoretail3-zip.18789/
Make sure that header of rom you write to sky has same header as game from save comes from. Edit template .txt accordingly
hello again, Retail to Sky3DS option added, with option to input own Online header from retail cart for save to match, or auto add from template. report bugs here. ill fix later :)
thank you all.
Card ID is the online header ;) if its FF its erased meaning thats an offline game or scene release erased it. im adding auto save size detect to the program now. and thank you!
Done, please test, at the moment you need to select original save size! later i can add template auto search to know what is the correct size automatically.