Everything is updated, only thing is emummc went back to when it was when I modded the console.
At first (after modding the switch) whenever I used either sys or emu, it was literally the same thing, so doing one thing in one version (either installing a game, modify profiles, etc...) it would show the same changes in the other. So that made believe it was the exact same thing. So I played using sys, one day I mistakenly pressed update (thanks to annoying popup appearing every time I start a game), since then It gave me an error everytime I tried to load sys, so I continued on emu (again, everything that I did on sys, appeared also on emu)
Now after the update emu showed things as they were when I first modded it. sys still didn't work, but after using a guide for daybreak, sys worked smoothly, and all games, profile, etc... were showing as I left them before this update.
This is the whole story I think