How does it matter what header it's using? It's still a valid header, the Save Data Transfer Tool should accept it just fine.
Using the 3DS' native save backup / import wouldn't work. Which is what my response was to.
Going from one header to another via the 3DS' native save backup would result in a corrupted save file, or am I wrong?
Later (which I wasn't aware of) it was brought up, that OP could use Ninjhax + a beta save transfer tool that was made as a place holder (or it was just made prior to Smealums, idk) until Smealums sava data tool was released.
So i'm not entirely sure why you're quoting my post now, after OPs question question has been answered and a solution provided.
Edit: Unless I was mistaken, OP was referring to the 3DS' native save backup.
Edit: Yeah.. http://en-americas-support.nintendo...d/73/~/how-to-use-the-save-data-transfer-tool