The NTRBoot flasher works fine, it backed up the flash from my card, but I was trying the R4 SDHC 2016 Gold Pro (one of the dual core carts I believe?) with the R$i SDHC flasher made to revert the B9S cart.
Don't use their flasher then, use the modified ntrboot_flasher from @AngelSL to write the r4i-b9s backup to it and tell us if it worked.