Broke FileHistory in Windows 8.1 - how to fix?

I recently discovered the Windows 8.1 FileHistory feature when I was looking for Backup. I configured it to use an external USB drive and turned it on. I soon observed that it was eating up space way too fast. I realized the was the virtual
machines I run. The VHD files can be 30GB or more any every time I ran them I would get yet more copies of these huge files in my file History. I excluded the VM folders from file history and set up an XCopy job instead that kept only the most
recent versions of my VM files.
But excluding the VM folders did not remove the VM copies that had already been made. So I went into the backup drive to manually delete them. But I accidently deleted the entire FileHistory backup for the C drive.
A few days later I checked hoping that FileHistory had made new backups of everything, but I only found files which were new or updated since I went around the app and did the mass-delete.  I tried turning FileHistory off & on again and
reconnected the backup drive, but I'm still seeing only new and updated files added to the archive.  
Finally I did a test my copying files that have been on my desktop for a while back into the FileHistory Desktop folder, and then trying to restore them (BTW, all the items I deleted still appear in the "Restore personal files"
screen, but can't be restored.   I get an error "Could not find this item" even though I put the item back.  So apparently deleting archive files from outside the FileHistory App breaks the link between FileHistory's database
and the actual archived files.
So how do I fix this?

Hi,
Please take a try to use clean up versions, we could only keep the latest one:
Under Control Panel\All Control Panel Items\File History\Advanced Settings, click clean up versions, then select one option listed.
The error occurred because the item is not stayed in the folder, and if we move the right item back, it could still be restored.
More information about file history, please see:
What if something goes wrong in File History?
Windows 8: File History explained
Best regards
Michael Shao
TechNet Community Support

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