First of all, I take responsibility for causing this, because I did something Nintendo warns against and just wasn't paying attention.
I recently transferred from an Original 3DS XL to a New 3DS XL. The card slot on my computer was having trouble recognizing the micro SD card and adapter that I wanted to use in the new system for some reason. After a few hours of trying to find a solution I had the idea of putting the micro SD card into the New 3DS and transferring my save data from my PC wirelessly (I had been able to copy this to my PC after transfer). I now know that this only works for photos and music, but I didn't at the time, and it seemed to be working.
Once that was finished, I tried downloading and opening Super Smash Bros. 3DS, only to find that my save data was gone. The game created new save data, but I deleted it. I got a functional SD card reader and transferred my save data to the micro SD card from my PC. Now all of my save data is there. However, when I opened Super Smash Bros. 3DS to test it, I received the message, "Unable to use the save data since it is not the latest data." I was asked to create new save data, but for now I said No.
Is there anything I can do to get my original save data to be functional again?
Thanks.