Yeah…
I tried flatpak update -v with no luck. sudo flatpak repair and then reboot does not work either. flatpak uninstall --all it is. Then, I just used Déjà Dup to restore the app configurations, that I had backup.
Also. Thanks for recommending Flatsweep, that is the coolest thing I got out of all of this.
I do most things via flatpakk by default. It provide an aditional layer of reliability to the apps I use. When somehing goes wrong, with a new update or st like that, it would just break the app rather than my entire system. The sandboxing is definitely a plus when using something like WINE, as a lot of games/apps required a specific version of it. Managing them when they are installed natively is really stressful, since mistake there can break you system as well. All of these Flatpak benefits is doublely important when I recommend Linux to less tech-savy people, i.e. my cousin/mom.
Nevertheless, there are apps that have worse-that-native flatpak version, or required to be native to be full-featured (system configuration, i.e. Dconf).
It is ok. The corruption happened because I was trying to revert to a back up on mass (restoring my entire Home directory)