If you nuke your system save data, you need to reinstall reinstall your games. The files on sd card only work because they were registered in the title database on nand, if you wipe and start over from scratch then the games arent in title database anymore and the os won't even try to read them (in fact it will tell you there is incompatible data and you need to delete it.)
You might be able to keep system save data 8000000000000120 (system titles) and 8000000000000121 (installed games, updates and dlc), and maybe 8000000000000122 too? I don't know what that one does. Those three are the system save data for the system module that does content management, if you keep 8000000000000121 then your installed games remain registered in the title database and maybe you can avoid having to reinstall them. If you do this then you probably want to keep system save data 80000000000000E0-E1-E2-E3-E4 (5 files) because those relate to tickets for installed stuff, if your games updates or dlc had tickets then you need to keep them there or they wont work anymore. You might need to keep 800000000000004A too, I'm not sure if rightsid matters for non-legit content
It goes without saying I have no idea what I'm doing here, I've never done a partial wipe like this on switch so I don't know what's important to keep or not. It's possible the save data I mentioned here relies on some other save data (it's not all well documented) and that things could crash if all the right save data isn't where it expects it. So to guarantee things will work as expected (assuming your sd card isnt bad and there is no hardware damage), for emummc issues I really just recommend wiping it and starting a new emummc, because then you know you're restarting from a known good state
Do keep a backup of your current emummc and sd card data though, that way if starting over doesn't work or you're unhappy with the change for any reason, you can restore back to where you were. For save data, I guess technically the files on user partition in the saves folder could be sufficient, but really you should use some kind of homebrew app to backup the save data to the raw actually readable files (with jksv or checkpoint, or dbi, whatever you like), because restoring save data later will be a lot easier with them