tbh it's hard to tell what's actually happening, if it's just my configuration that's wrong or if the emummc in your sd card is actually bad
it's possible too that your hidden partition you have there doesnt actually contain a valid emummc or it contains a corrupted one, and you had been using file-based emummc this whole time (which yes, if you deleted emummc folder, that would have been deleted)
but we cant really know that since the files are gone and we cant check anymore
tbh I would kind of just go a different direction entirely right now
hopefully you're on windows so you can use nxnandmanager
https://github.com/eliboa/NxNandManager/releases
then do this to mount that partition in the program
https://github.com/eliboa/NxNandManager?tab=readme-ov-file#emunand-partition
hopefully there is a valid emummc in there and it will be mounted. then I would do a full dump to backup the emummc to a file on your computer
after that, I would backup everything on the sd card, then in hekate, reformat the card for emummc to create a fresh partition emummc, this will configure everything correctly for that emummc partition which will ensure the configuration is correct (which mine might not have been)
then I would boot into that emummc just to confirm that works fine, to rule out sd card or partition problems. when you know that works, I would mount the emummc in nxnandmanager again, except this time restore your backup you made earlier
hopefully then you will be back to a state where the configuration is correct, and your old emummc is functional again. but that assumes that the contents of your hidden partition are good and nothing is corrupted
it's possible too that your hidden partition you have there doesnt actually contain a valid emummc or it contains a corrupted one, and you had been using file-based emummc this whole time (which yes, if you deleted emummc folder, that would have been deleted)
but we cant really know that since the files are gone and we cant check anymore
tbh I would kind of just go a different direction entirely right now
hopefully you're on windows so you can use nxnandmanager
https://github.com/eliboa/NxNandManager/releases
then do this to mount that partition in the program
https://github.com/eliboa/NxNandManager?tab=readme-ov-file#emunand-partition
hopefully there is a valid emummc in there and it will be mounted. then I would do a full dump to backup the emummc to a file on your computer
after that, I would backup everything on the sd card, then in hekate, reformat the card for emummc to create a fresh partition emummc, this will configure everything correctly for that emummc partition which will ensure the configuration is correct (which mine might not have been)
then I would boot into that emummc just to confirm that works fine, to rule out sd card or partition problems. when you know that works, I would mount the emummc in nxnandmanager again, except this time restore your backup you made earlier
hopefully then you will be back to a state where the configuration is correct, and your old emummc is functional again. but that assumes that the contents of your hidden partition are good and nothing is corrupted