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Sorry I haven't got to the root cause, but there is a real problem so I shall log what I have seen.
I have written a new Page in WLW, set the Page Parent to a page within my site (/Projects), and clicked "Post draft to blog".
When I look in the site, my "Home" page has been moved to the location of the page I wanted to create, and my post has been added to it. The Home page has disappeared from the root of the site - it really has been moved such that its parent is now /Projects.
The content feature that was previously on my Home page has been deleted without trace, and replaced with the new HTML content feature (which has been correctly named after my WLW post name - this did not duplicate the original feature name). Fortunately I've managed to reconstruct this using Google's cached page.
I'm reluctant to do too much experimenting at the moment, because of having to repair the site each time. If I learn more about the cause I'll post. I suspect it's either something to with using "Post draft" instead of "Publish", or perhaps caused by having pages in the site with duplicate page names.
If you can produce the problem on our demo site and provide detailed steps for me to reproduce the problem I will look into it.
Unable to replicate on the demo site, but my site is a bit weird with lots of different permissions and some pages with duplicate names etc. I'll post if I find out any logic.