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Shant - I assume you have no backup <sigh>
Make sure you're logged in as an administrator. Turn UAC off, in control Panel Folder Options->View select Show Hidden drives, folders and files, and uncheck Hide protected operating system files.
In windows explorer navigate to your 3TB drive. In search enter
"metadata.db", theoretically that will tell you where all all your libraries are - also search for an author eg "
Daniel Defoe" and for a book name "
Moll Flanders" that might lead you to where they're hiding.
If you don't want to use Windows Search you could use this ==>>
Search For Folders and Files -- it does not have to be installed just unzip it.
But I suspect something is broken - you could try a System Restore or running chkdsk, see ==>>
The How-To Geek Guide to Using Check Disk in Windows 7
BR