Sorry this happened. It seems that this time you accidentally deleted the entire .adds/koreader/ folder?
With wifi enabled, you should be able to update over-the-air using the built-in Update feature (top menu, 3 horizontal bars in corner, Update). I don't think the one-click packages are meant for updates.
For future reference, the KOReader User Guide has a section on how you can back up and restore your settings:
http://koreader.rocks/user_guide/#troubleshooting
Further down: Backing up your KOReader settings