if you write the nand back to the 3ds and start it then read it back then the hash will be different as the 3DS changes stuff on the system every time it boots
to check if the FIRM downgrade process is being done open the original nand backup and the "modded" on in a hex editor and go to the offset 0x0B130000, and make sure that there is some differences, im not100% sure what first offset than changes, but its around 0x0B130005, but side by side there will be obvious changes in that area