https://imgur.com/Pc4DQE5,f1wqDJD
XIGNCode won't work without x3.xem and xnina.xem, deleting those will give you this XIGNCode error when starting the game (before the game even loads). You can see it re-created xm.exe and xmag.xem, but not the others.
I like the file cleaner, it's clean and works well, but you should remove the options to delete x3.xem and xnina.xem next time.
Edit: I made a backup of the XIGNCODE.USA folder before deleting anything, so I was able to restore it. I suggest anyone that uses this, any other file cleaner, or deletes anything from the XIGNCODE.USA folder to do the same in case it breaks.