System restore to before using Citra emulator.

Also, write, post, complain to the Citra authors. Remember that NO ONE HERE may know what this did to your system.

As to the issue of "can't lose" if that is true where is the full system backup? You create this when the system is just as you wish. Also, if you have apps you can't reinstall, those are put on your list of "things I gotta find or find the installer" as someday malware or hardware will take out this PC.