Attention: I don't know if FSToolbox produce a different dumps than the USBloaderGX+d2x dump!
Some filename on the NAND contains incompatible FAT32 characters which are replaced on the emuNand with html entities by d2x. (that's why some Nand dump doesn't work with EmuNand and you need to make a new dump using the internal dump feature).
You can't just copy/paste the files as is on the real nand. You need to be sure it's using the correct naming convention before writing back to the NAND.
It's rare that they are using incompatible characters, but it happens, so double check before writing to nand.
Maybe using SavegameManagerGX is the best solution, as it create a text file which stores the real filename.
Be sure to have at least a save on your Real nand.
Export your save from Real nand, to create the correct file and folder structure and filename.
Replace the files from your emunand title/000x000x/GameID/data/ (different depending on the game type: Disc, Channel, VC/WiiWare, etc.), and match the filenames from SD:/savegames/ folder.
You could also try FTPii so you can rename the files on the nand and set permission if needed. (but I had some problems with FTPii, so it's dangerous to write to nand)