ROM Hack Pokemon OR/AS Save problem.

[Xeogran]

Hello there! I'm playing around with the Pokemon Omega Ruby 3DS ROM. Since it has the .3ds extension, it's on the Gateway Red Card and not on the SD Card.

Now, everytime I rebuild the ROM and replace the old one with a new, my save file stops working and I need to go through the SaveDataFiller process all the time (New Game -> Extracting the save then replacing it).

Is there a more simple way to keep one save file without going through the kinda bothersome process everytime I want to check how my Hack has turned out?

Thanks.