I'd just start from scratch in that case. If you're using hidden partition emuNAND, it might be enough to just delete the SD card contents and start with a fresh Atmosphere, Hekate, sigpatches, etc. so see if that would work in your case. Backup your SD card contents (you don't need to backup games as you can reinstall them at any time, I suggest that you do it via
DBI installer).
Make sure to test your SD card with
h2testw before you proceed. Note that the bigger the card, the more time it'll take for the app to test it. If there are no errors, you can use that card. Otherwise, you'll probably need to buy another one unless you want to risk another data corruption.
I've recently replaced my 128GB ADATA with the 256GB Sandisk Extreme microSD card because the first one would every once in a while throw a data corruption error so it was only a matter of time when will I run into it again (it happened about two times before I replaced my microSD card).
I'd suggest that you follow either
this or
this guide. Additionally, you can grab
sigpatches and/or
sys-patch module so that you can play game backups.
Before installing mods, I'd suggest that you make a backup of you SD card contents, just in case they corrupt your files again.