You're right that this problem is not exactly an installation issue but rather something that can happen pretty much anytime during the lifetime of OOo (for root causes unknown, otherwise we'd have fixed it ;-)), and that a repair/uninstall/reinstall will not fix.
Sorry, I did not review the installation issues since I was not having an installation problem. But it would seem that this type of issue could be easily resolve through the repair process or the remove/install process.
The reason these steps do not correct the issue is that they solely deal with the parts of OOo they were responsible for creating, i.e the initial post-installation structure. The contents of the user subtree are for the most part generated during the course of the user interaction with OOo, and the only thing a process could do would be to remove them altogether, which arguably in this situation would be a lesser evil.
In the 2.0 release, the error handling of the configuration component has been improved so that it's much more resilient to these situations and takes appropriate steps to allow the application to keep working (though if such an issue still occurs, the preferences stored in Common.xcu would still be lost).
I've submitted issue 46728 about the location of that FAQ. I suggest to move it (or link to it) in the General section.
Thanks for the feedback,
Cyrille
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