I had the same issue.
I solved it by inserting my sd card into a 'windows computer' and deleting the gm9 folder.
I redownloaded the same version of godmode9 and put the gm9 folder on to the root of my sd card.
I put the setup_ctrnand_luma3ds.gm9 and the cleanup_sd_card.gm9 in the scripts folder...