I first reported this problem back in June. Now it has happened at least 3 times to users over the last few days (with different missing keys).
About time the problem was fixed (search on appSettings).
Given that the problem appears to be in Windows Installer (it is completely responsible for updating the files on disk during an upgrade), we can't reproduce it here, and it has a fairly simple workaround (Repair the installation from Control Panel), we will be prioritising fixing other bugs above this one.
Edit: And it just happened again. There's something weird definitely happening with this particular upgrade; we should investigate further.
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