I think what you'll want to do is copy your original nand.bin (nand backup) to your SD card and use either EmuNand9 or Decrypt9 and select the option to dump the nand.bin to your emunand. This should replace the emunand with your original nand and allow you to use your files from before.
Make sure to turn off the 3DS as soon as everything's finished, and DO NOT START UP EMUNAND until you've copied your original files over. Make sure you have all of the files from your Nintendo 3DS folder backed up or else this won't work (your profile and saves are in there).
I haven't tried it myself but I'm in the process of doing something like that because my backup saves are not showing up (using different profile ID).
*EDIT* In case anyone else reads this, yes this works. I was able to use my original saves, backup saves, eshop downloads, everything. Just be sure you have your original sysnand backup or you won't be able to gain access. If you have that you can replace the emunand with your sysnand by selecting Clone Nand.bin to Emunand with Emunand9.