After the latest update the config window and icon seems to be gone. The upgrade tool still upgrades in accordance to the last set config, but I can find no way to create a new one/update the current one.

Could you see if you accidentally triggered the hide button keybinding (defaults to ctrl+u) and if not could you maybe upload the safe as I can't reproduce the problem.
Thanks!

Ctrl+u was the issue. I failed to realize it as all the other UI elemts from other mods were present. Thanks for the help and appreciate the work!