I think that I’m in a similar or the same situation. With eShop shutting down soon, I decided to do what I thought was the ‘responsible’ thing and back up all of my 3DS software to a spare micro SD card. I did not know that this would corrupt the save data of my VC Pokémon games; lesson learned, the hard way.
Now I’m looking into setting up my 3DS with homebrew and my question is this: if I have my original 3DS backup data stored on my PC, can I restore it to a micro SD card, insert it into my 3DS and access my original save data without it being corrupted? If I understand correctly, this could be done by deleting the game’s SecureValue with SaveFL?
Any feedback is appreciated, thanks for putting up with my noobiness!