Sometimes when handling the Switch's SD card files, some of the files can get their Archive bit removed automatically, which may cause the Switch to no longer recognize said files (like the ones inside the Nintendo folder). This can happen when handling the SD's data in other OS, like Linux or Mac (and sometimes even on Windows too).
This can be easily resolved by fixing the archive bit on the files on the SD card.
Fixing that archive bit with
Hekate 5.3.3 or above (Under the "Tools" option) effectively restores said bit to all your SD Card's files for Switch usage.