So far I have not detected the disappearance of any core files, only pages sent to the trash and recoverable and images (probably PDF downloads) which are not recoverable. You can still see the evidence of the missing images at http://www.pupconsortium.net
Yes, the are gone from the library completely.
I used automatic and then re-installed automatically. Aside from the numerous deleted files, the setting for the homepage had been switched from static to posts. Fortunately I could easily change that back and now have my home page again, although with numerous missing images.
