Recovered user profile Empty folders with hidden data

CapU
Contributor III

Yesterday a tech came to me and informed me that an Instructor had brought in her laptop. She was using Mail and it no longer was sending. "She's using Mail?" I thought. Its been a while since any our users have used Mail. I figured that it had to be an old setup and asked the Tech to just install the updates for the OS. He comes to me a little panicky saying that the Machine was installing Mavericks.
"What?" 1: The instructor had not done any updates...since 2013
2: The instructor was a local user and not a domain user.
3: The instructor had several user folders.
We backed up her profile to an external drive
After the update we put the folder back, and re-created the user on the laptop. Thats when I discovered that her account was actually local and had a different name from her domain account.
We decided to clean up the Users folder as there were several of her profile folders with the word deleted
After determining the correct folder we deleted her user account selecting Don't change home folder.
I changed the permissions on her profile folder to allow her network account access. After logging in as her the keychain went crazy. I tried to fix the keychain but it would freeze continuously. After several attempts to fix the keychain, I force quit Keychain Access then rebooted the laptop.

I logged in with our local admin account and noticed that now the Applications folder was almost completley empty. And the folder we backed up looked empty. I typed in the command to unhide files and there they were...
443cb0d3713e45b894d89ae506760b2b
I found a program to help me rename the files they ALL have a leading . in the name.
Has anyone else seen this before?

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