yes, you use the hardmod to take a backup of your current nand, then apply the b9s to that backup, then flash it back to your 3ds. now you can boot .firm payloads from SD indepedantly of your nand FW. use that to load Luma and chainload Godmode9 to CTR transfer, to fix your FW.
edit: or if you want to wait, you can wait for ntrboothax that will allow you to boot .firm payload from a NDS flashcart (which ones will work has not been announced yet) but you will need a CFW 3ds to install it to the cart. then your 3ds will boot immediately from that cart, load godmode9 and you can CTR transfer and fix your FW