I have no idea where you are in the A9LH guide, and where your "important" NAND is; sysNAND or emuNAND. Until you answer those, I won't be able to help you.
If there's nothing on the SD that you care about (including emuNAND), copy the SD card's files (all of them) to a safe folder on your computer, and then format it with Disk Management (remove the emuNAND Unallocated Sector and Current FAT/FAT32 Partition, and then create a FAT partition, and COPY (not CUT!) your 3DS files back into your SD. After that, format the SD card on the 3DS for emuNAND use when asked to do so, and put the files back right after formatting (the guide details these steps).