Oh my friggin god. Back up your SD Card, Get a NTR-Boot compatible NDS Flashcart, then do NTR-Boot to install Boot9Strap, then put the latest version of Luma3DS on your SD Card, and do the same with GodMode9. Then, after all that is done, reboot your 3DS, and if you DON'T see the Luma Config menu, Force your 3DS to shut Off, power it on again, this time holding SELECT. Then, make sure that the ARM Exceptions option is enabled. Turn off your 3DS, then power it on again while holding [L], [R], (A), and [+UP] (+ is the D-Pad) This should take you into the Recovery Menu, which is built into ALL 3DS Systems, H'Brew'd or not. From there, you should be able to perform a system update, which should restore any missing System titles, even the ones on TWLNand! If that don't work, then I hope to heck it's a 2DS or New 3DS so you can send it to ninty.