Documents missing

All of my file stored in document folders seem to be missing. They appear in VO under the document libraries, however, after clicking on them I get:
Error!
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If I use the web folders (from windows) I see the folders, however, there are no files.

I check serveral backup ZIP files as well as a complete TAR file that I made of the VirtualOffice folder I made several months ago. When searching I find documents from attachments, however, I do not find any documents from personal and group shared folders.

Are the files stored in the database or are they stored in the file system.

I may have just lost months worth of work. Is there any hope?