I would suggest checking for a corrupt SD card, first of all, even if it does boot godmode9, if corrupt, it can still do some weird stuff. The next thing i would try is updating the CTRNand luma, and deleting the config on the nand. The problem that you were saying with godmode9 and trying to unlock access to delete the file is most likely a bug. You might want to try re-extracting the latest version from
https://github.com/d0k3/GodMode9/releases to your luma payloads folder on your sdcard, and renaming it to, for this, lets just say x_godmode9.firm, so you have to hold the X button instead, since according to Luma, whenever you use the R, A, Start, or select buttons, you also have to hold the L trigger to boot into that specific payload, which is why i said reassign it to the X key instead, then see if you still get the bug while attempting to delete luma's config.
Edit: Forgot to mention, you could also try setting up godmode9 as the boot.firm on the root of your sd card, since it has support for that with the latest updates, and that might fix the bug since it isn't running through the Luma chainloader to load godmode9. I'd recommend doing this instead, first, then trying to delete the configs for luma. Also, if you have any questions about setting up godmode9 as the main boot.firm, just PM me or reply to me here, and i'll get back to you next time I'm on gbatemp. Also note that after you delete the luma config file this way, if it does work, you will have to replace the boot.firm with the luma payload again. also note i do not mean installing godmode9 to the main firm partition, since that is where boot9strap is. Instead the instructions i gave are just bypassing luma's chainloader to see if that is causing any bugs.