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If you'd like to try with the fresh Hekate/Atmosphere/Sigpatches, you can keep that folder as that's where you games, saves, screenshots and alike are stored, among other things. The rest of the files, you can backup and delete afterwards, and download a fresh set of Hekate, Atmosphere and sigpatches and see if that will fix the issue you're having. If you manage to get it to work, I'd back up the save files with JKSV, copy them to PC and start from scratch afterwards, following one of the written guides that I've previously mentioned. Or, if you feel that's unnecessary and that your SD card is legit and the file corruption happened due to bad transfer (damaged cable, incomplete files, etc.), you can start filling up the SD card with all the homebrew you usually use and need.should i keep the emummc folder in the sd or should i delete everything
Anyway, that's what I'd do personally, as I'm not really an expert in troubleshooting other people's issues. Therefore, fresh install if possible is usually the way I suggest people to fix their stuff unless it's something really trivial.

I have seriously forgotten how I formatted my previous Switch SD card. In my defense, it's been a couple of years, andI have a bad memory 







