Setup backups everything he does changes to. The next time you apply for some different campaign, it first does a complete un-backup (return to original files), then backups again (it has a new list of files that will change, so we prevent 'left-overs' in backup folder like this), and applies changes.
The reason you have perma arrows not turning off can be simple - you had them turned on when you were playing 6.3, then you installed 6.4 and it deleted the backup folder because the file structure is different now. And so only the 'modified' ver left
