Hey, I have a similar issue with my Pokemon Yellow VC save. I made a mistake cloning my pokemon with the PC and now the save file is corrupted.
However, I installed CFW on my 3DS and was able to see the save file using Checkpoint. With PikaSav, I can load the file and I see all of my playthrough's data, so how do I correct the error to get it working on the VC again? Any ideas? There aren't really good tutorials about this on YouTube.
sav.dat