I recently got a Japanese 2DS. I have hacked other 3DS systems before, so I had no problem getting everything running on this one. Went through the guide step by step to be thorough, and changed the region after just so I could have the menus in English. At this point, I had encountered zero issues. I installed some 3DS games and homebrew programs with no problems, until I put on NDS Bootstrap, Twilight Menu, and NDS forwarder. Twilight menu wouldn't open, so I looked it up and saw that it sometimes has difficulty with region swapped consoles. Installed TWLFix and it finally opened. Everything seemed to be running fine, but when I connected the SD card to my computer, I was having issues moving files. Suddenly, the 3DS couldn't read the SD card anymore and when I put it back on my computer it was corrupted. I formatted and tried to start over, but it kept getting corrupted as soon as I put it in the 3DS.
It was an old SD card so I figured that could be the problem, and I got a brand new one. Went back through the motions, got homebrew running and everything just fine. I should probably note that, throughout this time, twilight menu stayed on my home screen even when there was no SD card inserted. Every other program disappeared of course. Once again, I had no major issues on this second go until I tried opening twilight menu. I encountered an error and twilight menu wouldn't launch so I reinstalled it from the universal updater. Now it launches just fine, except homebrew launcher and the universal updater crash on boot now, and my pc says the SD card is corrupted and can't read it. It actually crashed file explorer when I firest tried to open it. The picture is what I see when I try to open the updater. I also can't boot to luma or godmode anymore. The battery light just shines yellow until I take my finger off the start/select button.
If anybody has any advice, I would really like to hear it. Both corrupted SD cards are sandisk, 32gb for the first and 64 gb for the second (brand new) card. I am guessing the issue stems somehow from the twilight menu/region change/DS mode but I really don't even know where to begin here.