App icons became blank

I don't know exactly when, but some of my app icons became blank and some keep toggling between normal and blank. It looks like this:

This is my macOS version:

and since I've having a lot of bugs recently, I'm considering reinstall macOS on my MacBook. Is there a easy way to restore the data and applications back after reinstalling the system? I've made a macOS thumb drive with the newest version but I haven't done this on mac before and I don't know how to restore the data. Thanks!