Did you move anything around on the card? I save via the instant save as well just in case. Look for a .sav file somewhere on the card that had the same name.
I recently upgraded to the 3DS XL from a DSi. My main usage of the system is for the DS2 and it's related features but I also wanted a larger device and to play some 3DS games, hence my reason for switching.
Do you see any reason to keep my DSi or should I sell it if I can get a decent enough...
Apparently unlike the DS/DSi/XL the 3DS constantly polls the inserted cart. This is used for street/spotpass updates and and things of that nature but also works as a measure for anti-piracy. I am new to the 3DS (XL) and that was a bummer but it's easy enough to eject the cart when not in use...