In general, almost everything you install with pacman will update when you do pacman -Syu (and restart, in case of kernel updates). The way packages work, all the files needed for a piece of software to function are installed from a package, and when you install a newer version, it removes all the files from the old version and puts in new ones. (Caveats apply to configuration files you can modify - those don’t get replaced if you do)

So after you update some software through pacman, it should be in an entirely clean state, just like if you just installed it. The main caveats apply to things like flatpak, which manage its own packages, and software like Steam and Discord, which have an additional auto-updater for some things that’s storing files separately.