Hey buddy,
I had something similar recently when I upgraded to FW 8.1 - In my haste when installing I opted for the 8.1 install rather than the 8.1 (exFat) install. This created a mismatch between my Micro SD card (exFAT) and the installation type of my Switch (then in FAT32).
I don't know if any of the software remained playable however most titles stated they required the software be re-downloaded. I also noticed that even though I was booting into SXOS, the Album had corrupted and would just take me back to the main menu screen of the switch.
To fix this:
I backed up my SD card (all files) onto my PC
Used partitioning software to format my SD card to FAT32
Copied the backed up contents of my SD card back onto the SD card (now both switch and SD card are FAT32 allowing SXOS to operate correctly)
I used
ChoiDujourNX to re-update my Switch to 8.1 (exFAT)
I formatted my SD card back to exFAT and again copied the backed up files to it
I probably went a really long way around this however it kept me busy for a few hours
