Before I continue, I must say that this is completely my fault and could have been prevented had I done my reading before messing with files.
I decided to back up my save in Pokemon X (I downloaded it, and now know I should not have and cannot back up my save), so i copied all the files onto my computer. I played for a bit afterwards, saved, turned the system off. A friend needed a 4 GB sd card, which is what my pokemon save was on. So i figured I could just give him the 4GB to use and put my backup on the 2 GB which came with the 3ds.
Unfortunately due to some anti-cloning measures Nintendo put in I am unable to access my save, and receive the message "The saved data is not compatible with this version, so it can't be used." I am directed to refer to the manual, where I find out that I'm not supposed to back up my save because, well, this will happen.
So, I admit that this was all my fault, but I'd like to know if my 150+ hours of play time are salvagable, or if I should attempt contacting Nintendo. 