Windows: Automatic restart after update leads to corrupted installation

How to reproduce:

YOu need an online installer on Windows.
Fetch a remote update.
On the final page of the Updater there's a checkbox whether the user want to restart. Leave that checked.
Restart.

It seems that there's a timing issue with writing the settings, and reading them, leading to a corrupted state.

performed operations (before sort): 67
writing 1 uninstaller operations ...