Hi guys,
I recently finished system transferring from my old 3DS XL to my New 3DS XL; I followed Nintendo's official video on the process point by point. I opted to use the PC-transfer option. I connected my old 32GB SD card to my PC, copied over the Nintendo 3DS folder to the PC desktop. Then, I connected my new 32GB microSD card to my PC, and copied over the same Nintendo 3DS folder. Put the microSD card back into my New 3DS XL.
My profile such as Miis and streetpass data were all secure, but my digitally downloaded games, Super Smash Bros for 3DS and Monster Hunter 3 Ultimate, were not present on the home dashboard. So I redownloaded Smash (for free) off the Nintendo eShop and booted it up. However, there was no savedata for it, it booted up as if it was completely new. I haven't tried redownloading Monster Hunter 3 Ultimate yet, but I would only assume it's the same. Strangely enough, I did still have my savedata for Monster Hunter 4 Ultimate (thank goodness), which I have a physical cartridge of.
I just tried re-transferring the same data (Nintendo 3DS folder) again to the microSD card after formatting it using Nintendo's recommended SDFormatter, with Full(Overwrite) as the selected option. But still no luck.
At this point I'm pretty convinced that I won't be getting this savedata back, unless someone can give some suggestions otherwise.. 
Thanks.