I've run into this problem literally every time I've updated the software: I hold my root directory, settings, and library files on an external drive. After update, on first launch, the settings and library gets reset and I have to E-brake the launch with CTRL+ALT+DEL before relaunching and restoring the root directory.
Is there a setting that I can click so that whenever I update I don't have to deal with the auto-replication of files into my hard-drive, and emergency processes to restore the root directory??