Dionicio3, you can try to save a save (lol) from a 3DS cartridge, it will be save as .bin.I just tested and my copy of Pokémon HeartGold saved as a .sav on Checkpoint 3.7.4, so I'm not sure what your issue is
As I said, I'm not with a DS cartridge right now, so I can't test it. If the save from a DS cartridge is save as .sav will be easier to solve my issue.
Plus, my last post has a edit that I made in the exactly moment that you replied me, I don't know if you saw.